rs45501594

Variant names:

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_001378454.1(ALMS1):c.10628C>G(p.Thr3543Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,613,648 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0067 ( 3 hom., cov: 32)

Exomes 𝑓: 0.011 ( 111 hom. )

Consequence

ALMS1
NM_001378454.1 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:13

Conservation

PhyloP100: 1.63

Variant links:

Genes affected

ALMS1 (HGNC:428): (ALMS1 centrosome and basal body associated protein) This gene encodes a protein containing a large tandem-repeat domain as well as additional low complexity regions. The encoded protein functions in microtubule organization, particularly in the formation and maintanance of cilia. Mutations in this gene cause Alstrom syndrome. There is a pseudogene for this gene located adjacent in the same region of chromosome 2. Alternative splice variants have been described but their full length nature has not been determined. [provided by RefSeq, Apr 2014]

ALMS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008732915).

BP6

Variant 2-73572505-C-G is Benign according to our data. Variant chr2-73572505-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 221028.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Benign=10, Uncertain_significance=1}.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00667 (1015/152192) while in subpopulation NFE AF= 0.0105 (717/67972). AF 95% confidence interval is 0.00991. There are 3 homozygotes in gnomad4. There are 441 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALMS1	NM_001378454.1 link	c.10628C>G	p.Thr3543Ser	missense_variant	Exon 16 of 23	ENST00000613296.6	NP_001365383.1
ALMS1	NM_015120.4 link	c.10628C>G	p.Thr3543Ser	missense_variant	Exon 16 of 23		NP_055935.4	Q8TCU4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALMS1	ENST00000613296.6 link	c.10628C>G	p.Thr3543Ser	missense_variant	Exon 16 of 23	1	NM_001378454.1	ENSP00000482968.1		Q8TCU4-1

Frequencies

GnomAD3 genomes

AF:

0.00669

AC:

1017

AN:

152074

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00237

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00721

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00353

Gnomad FIN

AF:

0.00170

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.00861

GnomAD3 exomes

AF:

0.00664

AC:

1642

AN:

247312

Hom.:

AF XY:

0.00680

AC XY:

913

AN XY:

134240

show subpopulations

Gnomad AFR exome

AF:

0.00260

Gnomad AMR exome

AF:

0.00355

Gnomad ASJ exome

AF:

0.00968

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00482

Gnomad FIN exome

AF:

0.00140

Gnomad NFE exome

AF:

0.0105

Gnomad OTH exome

AF:

0.00550

GnomAD4 exome

AF:

0.0114

AC:

16640

AN:

1461456

Hom.:

111

Cov.:

AF XY:

0.0110

AC XY:

8026

AN XY:

727014

show subpopulations

Gnomad4 AFR exome

AF:

0.00182

Gnomad4 AMR exome

AF:

0.00385

Gnomad4 ASJ exome

AF:

0.00888

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00511

Gnomad4 FIN exome

AF:

0.00162

Gnomad4 NFE exome

AF:

0.0135

Gnomad4 OTH exome

AF:

0.0103

GnomAD4 genome

AF:

0.00667

AC:

1015

AN:

152192

Hom.:

Cov.:

AF XY:

0.00593

AC XY:

441

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.00236

Gnomad4 AMR

AF:

0.00720

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00312

Gnomad4 FIN

AF:

0.00170

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.00852

Alfa

AF:

0.0112

Hom.:

Bravo

AF:

0.00717

TwinsUK

AF:

0.0154

AC:

ALSPAC

AF:

0.0140

AC:

ESP6500AA

AF:

0.00321

AC:

ESP6500EA

AF:

0.0117

AC:

ExAC

AF:

0.00685

AC:

827

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0108

EpiControl

AF:

0.0113

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:13

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Benign:5

Sep 29, 2015

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 31, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 26239645, 25846608) -

Jan 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ALMS1: BP4, BS1, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Alstrom syndrome

Uncertain:1Benign:3

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 21, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 02, 2019

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

Potent mutations in ALMS1 are associated with a rare condition called Alstrom syndrome. It can cause excessive eating, insulin resistance. However, no evidence is found to ascertain the role of rs45501594 in Alstrom syndrome yet. -

not specified

Benign:3

Dec 14, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.Thr3542Ser in exon 16 of ALMS1: This variant is not expected to have clinical significance because it has been identified in 1.03% (1297/125086) of European c hromosomes including 12 homozygotes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs45501594). -

Aug 02, 2016

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The ALMS1 c.10625C>G (p.Thr3542Ser, alternative name c.10631C>G) variant involves the alteration of a non-conserved nucleotide. 4/5 in silico tools predict a benign outcome for this variant. This variant was found in 824/119494 control chromosomes (5 homozygotes), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0099462 (658/66156). This frequency is about 4 to 7 times the estimated maximal expected allele frequency of a pathogenic ALMS1 variant (0.0022361) for CYMO or Alstrom Syndrom, respectively. The allele frequency in the European (Non-Finnish) subpopulation suggests that this variant is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. The variant has been reported in patients with clinical features of Alstrom Syndrome, but without evidence of causality (ie co-segregation or functional studies). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign. -

Jan 25, 2017

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Monogenic diabetes

Benign:1

Feb 01, 2019

Personalized Diabetes Medicine Program, University of Maryland School of Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: research

ACMG criteria: BP4 (six predictors plus Revel score: 0.024; not using PP3's three predictors), BA1 (1% in gnomAD European population), BS2 (15 homozygotes in gnomAD), BP1 (missense variant when mostly truncating mutations)= benign -

Cardiovascular phenotype

Benign:1

Jan 03, 2019

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.027

T;.;.

Eigen

Benign

-0.066

Eigen_PC

Benign

-0.043

FATHMM_MKL

Benign

0.36

LIST_S2

Benign

0.52

T;T;T

MetaRNN

Benign

0.0087

T;T;T

MetaSVM

Benign

-1.1

PrimateAI

Benign

0.39

Sift4G

Benign

0.11

T;T;D

Vest4

0.31

MVP

0.22

ClinPred

0.014

GERP RS

3.6

Varity_R

0.075

gMVP

0.086

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over