1-79809161-G-A

Variant names:

• chr1-79809161-G-A
• rs6424674

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 0.446 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.248 AC: 10260 AN: 41384

American (AMR) AF: 0.521 AC: 7939 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2153 AN: 3462

East Asian (EAS) AF: 0.192 AC: 995 AN: 5176

South Asian (SAS) AF: 0.507 AC: 2445 AN: 4820

European-Finnish (FIN) AF: 0.607 AC: 6383 AN: 10516

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.530 AC: 35956 AN: 67896

Other (OTH) AF: 0.466 AC: 982 AN: 2106

Alfa AF: 0.507 Hom.: 9675

Bravo AF: 0.429

Asia WGS AF: 0.345 AC: 1195 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.21
DANN	Benign	0.65
PhyloP100		-2.9

Splicing

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

Other links and lift over

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