5-147824254-G-C

Variant names:

• chr5-147824254-G-C
• rs3777125

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 0.648 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.648 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

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.634

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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