rs10496191

Variant names:

• chr2-73446670-C-T
• rs10496191
• NM_001378454.1:c.1433-1290C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378454.1(ALMS1):​c.1433-1290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,956 control chromosomes in the GnomAD database, including 15,427 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (15427 hom., cov: 32)
• Consequence: ALMS1 NM_001378454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 15 publications found

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 Gene-Disease associations (from GenCC):

• Alstrom syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, PanelApp Australia, G2P, Orphanet, Genomics England PanelApp

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALMS1	NM_001378454.1	c.1433-1290C>T		intron_variant	Intron 7 of 22	ENST00000613296.6	NP_001365383.1
ALMS1	NM_015120.4	c.1433-1290C>T		intron_variant	Intron 7 of 22		NP_055935.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALMS1	ENST00000613296.6	c.1433-1290C>T		intron_variant	Intron 7 of 22	1	NM_001378454.1	ENSP00000482968.1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57921 AN: 151838 Hom.: 15368 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00714

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.334

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.382 AC: 58043 AN: 151956 Hom.: 15427 Cov.: 32 AF XY: 0.375 AC XY: 27871 AN XY: 74268

African (AFR) AF: 0.756 AC: 31305 AN: 41436

American (AMR) AF: 0.370 AC: 5656 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3462

East Asian (EAS) AF: 0.00716 AC: 37 AN: 5170

South Asian (SAS) AF: 0.150 AC: 723 AN: 4812

European-Finnish (FIN) AF: 0.243 AC: 2564 AN: 10558

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16201 AN: 67930

Other (OTH) AF: 0.331 AC: 698 AN: 2110

Alfa AF: 0.266 Hom.: 3329

Bravo AF: 0.410

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		-0.050
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10496191; hg19: chr2-73673798;