1-74769633-T-C

Variant names:

• chr1-74769633-T-C
• rs3931020

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 0.713 in 151,960 control chromosomes in the GnomAD database, including 38,738 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 0.71 (38738 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108227 AN: 151844 Hom.: 38708 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.713 AC: 108315 AN: 151960 Hom.: 38738 Cov.: 33 AF XY: 0.717 AC XY: 53232 AN XY: 74290

African (AFR) AF: 0.749 AC: 31062 AN: 41496

American (AMR) AF: 0.763 AC: 11641 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2155 AN: 3468

East Asian (EAS) AF: 0.783 AC: 4037 AN: 5158

South Asian (SAS) AF: 0.676 AC: 3254 AN: 4816

European-Finnish (FIN) AF: 0.701 AC: 7422 AN: 10590

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46457 AN: 67860

Other (OTH) AF: 0.671 AC: 1418 AN: 2112

Alfa AF: 0.694 Hom.: 140681

Bravo AF: 0.721

Asia WGS AF: 0.704 AC: 2439 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.70
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3931020; hg19: chr1-75235317;