NM_001378454.1:c.9914A>G

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001378454.1(ALMS1):c.9914A>G(p.Asn3305Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00356 in 1,614,066 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 65 hom. )

Consequence

ALMS1
NM_001378454.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 4.18

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008951098).

BP6

Variant 2-73550273-A-G is Benign according to our data. Variant chr2-73550273-A-G is described in ClinVar as [Benign]. Clinvar id is 393379.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-73550273-A-G is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00236 (359/152306) while in subpopulation SAS AF= 0.024 (116/4828). AF 95% confidence interval is 0.0205. There are 2 homozygotes in gnomad4. There are 193 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALMS1	NM_001378454.1 link	c.9914A>G	p.Asn3305Ser	missense_variant	Exon 13 of 23	ENST00000613296.6	NP_001365383.1
ALMS1	NM_015120.4 link	c.9914A>G	p.Asn3305Ser	missense_variant	Exon 13 of 23		NP_055935.4	Q8TCU4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALMS1	ENST00000613296.6 link	c.9914A>G	p.Asn3305Ser	missense_variant	Exon 13 of 23	1	NM_001378454.1	ENSP00000482968.1		Q8TCU4-1

Frequencies

GnomAD3 genomes

AF:

0.00234

AC:

356

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00235

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0234

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00248

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00534

AC:

1332

AN:

249250

Hom.:

AF XY:

0.00667

AC XY:

902

AN XY:

135210

show subpopulations

Gnomad AFR exome

AF:

0.0000646

Gnomad AMR exome

AF:

0.00244

Gnomad ASJ exome

AF:

0.00258

Gnomad EAS exome

AF:

0.000780

Gnomad SAS exome

AF:

0.0265

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00319

Gnomad OTH exome

AF:

0.00529

GnomAD4 exome

AF:

0.00368

AC:

5384

AN:

1461760

Hom.:

Cov.:

AF XY:

0.00449

AC XY:

3265

AN XY:

727180

show subpopulations

Gnomad4 AFR exome

AF:

0.000329

Gnomad4 AMR exome

AF:

0.00300

Gnomad4 ASJ exome

AF:

0.00337

Gnomad4 EAS exome

AF:

0.000479

Gnomad4 SAS exome

AF:

0.0270

Gnomad4 FIN exome

AF:

0.000131

Gnomad4 NFE exome

AF:

0.00222

Gnomad4 OTH exome

AF:

0.00386

GnomAD4 genome

AF:

0.00236

AC:

359

AN:

152306

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

193

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.000361

Gnomad4 AMR

AF:

0.00235

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0240

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00248

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00269

Hom.:

Bravo

AF:

0.00184

TwinsUK

AF:

0.00297

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.000261

AC:

ESP6500EA

AF:

0.00448

AC:

ExAC

AF:

0.00596

AC:

720

Asia WGS

AF:

0.0130

AC:

AN:

3478

EpiCase

AF:

0.00376

EpiControl

AF:

0.00445

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Mar 21, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.Asn3304Ser in exon 13 of ALMS1: This variant is not expected to have clinical significance because it has been identified in 2.76% (455/16484) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitut e.org; dbSNP rs142022233). -

Jan 02, 2018

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.9911A>G (p.Asn3304Ser; alternative nomenclature c.9917A>G, p.N3306S) variant involves the alteration of a conserved nucleotide. 2/3 in silico tools predict a benign outcome for this variant. This variant was found in 1363/276886 control chromosomes, predominantly observed in the South Asian subpopulation at a frequency of 0.026704 (821/30744), including 19 homozygotes. This frequency is about 12 times the estimated maximal expected allele frequency of a pathogenic ALMS1 variant (0.0022361), suggesting this is likely a benign polymorphism found primarily in the populations of South Asian origin. An internal specimen also carries a pathogenic MYBPC3, supporting the benign role of the variant. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign. -

Jan 24, 2017

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:2

Feb 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: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Alstrom syndrome

Benign:2

Sep 16, 2020

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 31, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Monogenic diabetes

Benign:1

May 18, 2018

Personalized Diabetes Medicine Program, University of Maryland School of Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: research

ACMG criteria: [BP4 (3 predictors) PP3 (6 predictors) Revel score 0.193: conflicting data, not using], BS2 (20 homozygotes in gnomAD, all but 1 South Asian), BS1 (2.67% in South Asians in gnomAD), BP1 (missense variant when truncating is disease causing) (Partners/Invitae/GeneDx all call benign but no longer using BP6)= benign -

Cardiovascular phenotype

Benign:1

May 30, 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

0.20

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.15

T;.;.

Eigen

Uncertain

0.53

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Uncertain

0.87

LIST_S2

Uncertain

0.91

D;D;D

MetaRNN

Benign

0.0090

T;T;T

MetaSVM

Benign

-1.2

PrimateAI

Benign

0.47

Sift4G

Benign

0.45

T;T;T

Vest4

0.40

MVP

0.39

ClinPred

0.048

GERP RS

5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.12

gMVP

0.25

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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