chr5-147824254-G-C

Variant names:

• chr5-147824254-G-C
• rs3777125

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 0.648 in 152,024 control chromosomes in the GnomAD database, including 32,269 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 0.65 (32269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98401 AN: 151906 Hom.: 32234 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.648 AC: 98496 AN: 152024 Hom.: 32269 Cov.: 32 AF XY: 0.654 AC XY: 48607 AN XY: 74294

African (AFR) AF: 0.680 AC: 28182 AN: 41454

American (AMR) AF: 0.624 AC: 9535 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2163 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4175 AN: 5142

South Asian (SAS) AF: 0.823 AC: 3969 AN: 4824

European-Finnish (FIN) AF: 0.702 AC: 7416 AN: 10568

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41032 AN: 67982

Other (OTH) AF: 0.634 AC: 1336 AN: 2108

Alfa AF: 0.630 Hom.: 3602

Bravo AF: 0.643

Asia WGS AF: 0.817 AC: 2838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.38
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs3777125; hg19: chr5-147203817; COSMIC: COSV57024346;