rs474939

Variant names:

• chr1-182569480-A-G
• rs474939

Variant summary

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

The variant allele was found at a frequency of 0.895 in 151,952 control chromosomes in the GnomAD database, including 61,323 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 0.89 (61323 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.895 AC: 135892 AN: 151836 Hom.: 61290 Cov.: 28

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.895 AC: 135978 AN: 151952 Hom.: 61323 Cov.: 28 AF XY: 0.893 AC XY: 66340 AN XY: 74260

African (AFR) AF: 0.904 AC: 37444 AN: 41410

American (AMR) AF: 0.857 AC: 13059 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3101 AN: 3472

East Asian (EAS) AF: 0.493 AC: 2523 AN: 5122

South Asian (SAS) AF: 0.903 AC: 4348 AN: 4816

European-Finnish (FIN) AF: 0.941 AC: 9947 AN: 10576

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62602 AN: 68008

Other (OTH) AF: 0.889 AC: 1873 AN: 2108

Alfa AF: 0.903 Hom.: 59370

Bravo AF: 0.882

Asia WGS AF: 0.756 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs474939; hg19: chr1-182538615;