rs2479394

Variant names:

• chr1-55020391-G-A
• rs2479394

Your query was ambiguous. Multiple possible variants found:

• chr1-55020391-G-A
• chr1-55020391-G-T

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 0.663 in 152,062 control chromosomes in the GnomAD database, including 33,891 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 0.66 (33891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 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: 0.664 AC: 100831 AN: 151942 Hom.: 33887 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.663 AC: 100877 AN: 152062 Hom.: 33891 Cov.: 32 AF XY: 0.660 AC XY: 49038 AN XY: 74332

African (AFR) AF: 0.613 AC: 25436 AN: 41468

American (AMR) AF: 0.598 AC: 9139 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2442 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2136 AN: 5140

South Asian (SAS) AF: 0.563 AC: 2712 AN: 4816

European-Finnish (FIN) AF: 0.741 AC: 7849 AN: 10586

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48933 AN: 67976

Other (OTH) AF: 0.647 AC: 1366 AN: 2112

Alfa AF: 0.690 Hom.: 164565

Bravo AF: 0.648

Asia WGS AF: 0.516 AC: 1795 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	2.7
DANN	Benign	0.34
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs2479394; hg19: chr1-55486064;