rs6424674

chr1-79809161-G-Achr1-79809161-G-T

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 0.446 in 151,806 control chromosomes in the GnomAD database, including 16,632 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 0.45 (16632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67692 AN: 151688 Hom.: 16637 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.446 AC: 67697 AN: 151806 Hom.: 16632 Cov.: 32 AF XY: 0.450 AC XY: 33370 AN XY: 74176

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.466

Alfa AF: 0.506 Hom.: 8616

Bravo AF: 0.429

Asia WGS AF: 0.345 AC: 1195 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.21
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6424674; hg19: chr1-80274846; COSMIC: COSV59960545;