1-74769633-T-C

Variant names:

• chr1-74769633-T-C
• rs3931020

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.713 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

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.671

Alfa AF: 0.688 Hom.: 61640

Bravo AF: 0.721

Asia WGS AF: 0.704 AC: 2439 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3931020; hg19: chr1-75235317;