1-161302651-A-G

Variant names:

• chr1-161302651-A-G
• rs4657015

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 0.633 in 151,394 control chromosomes in the GnomAD database, including 30,742 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 0.63 (30742 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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: 0.633 AC: 95831 AN: 151284 Hom.: 30711 Cov.: 30

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.633 AC: 95908 AN: 151394 Hom.: 30742 Cov.: 30 AF XY: 0.637 AC XY: 47085 AN XY: 73908

African (AFR) AF: 0.699 AC: 28870 AN: 41290

American (AMR) AF: 0.687 AC: 10466 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2104 AN: 3460

East Asian (EAS) AF: 0.727 AC: 3756 AN: 5166

South Asian (SAS) AF: 0.662 AC: 3186 AN: 4814

European-Finnish (FIN) AF: 0.625 AC: 6420 AN: 10266

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39213 AN: 67880

Other (OTH) AF: 0.608 AC: 1271 AN: 2090

Alfa AF: 0.596 Hom.: 108497

Bravo AF: 0.640

Asia WGS AF: 0.704 AC: 2415 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.42
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4657015; hg19: chr1-161272441;