rs3925058

Variant names:

• chr1-47331951-G-A
• rs3925058

Your query was ambiguous. Multiple possible variants found:

• chr1-47331951-G-A
• chr1-47331951-G-C
• chr1-47331951-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 0.575 in 151,904 control chromosomes in the GnomAD database, including 27,268 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 0.58 (27268 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.575 AC: 87283 AN: 151784 Hom.: 27232 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.575 AC: 87366 AN: 151904 Hom.: 27268 Cov.: 31 AF XY: 0.569 AC XY: 42228 AN XY: 74216

African (AFR) AF: 0.831 AC: 34468 AN: 41486

American (AMR) AF: 0.569 AC: 8665 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1181 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2846 AN: 5146

South Asian (SAS) AF: 0.449 AC: 2160 AN: 4812

European-Finnish (FIN) AF: 0.356 AC: 3744 AN: 10526

Middle Eastern (MID) AF: 0.445 AC: 129 AN: 290

European-Non Finnish (NFE) AF: 0.479 AC: 32557 AN: 67942

Other (OTH) AF: 0.537 AC: 1132 AN: 2108

Alfa AF: 0.551 Hom.: 25778

Bravo AF: 0.605

Asia WGS AF: 0.507 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs3925058; hg19: chr1-47797623;