rs951436

Variant names:

• chr1-163063552-A-C
• rs951436

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 0.417 in 151,964 control chromosomes in the GnomAD database, including 14,238 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 0.42 (14238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63403 AN: 151846 Hom.: 14249 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.417 AC: 63397 AN: 151964 Hom.: 14238 Cov.: 32 AF XY: 0.417 AC XY: 30968 AN XY: 74266

African (AFR) AF: 0.239 AC: 9913 AN: 41486

American (AMR) AF: 0.478 AC: 7284 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1590 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2539 AN: 5134

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4814

European-Finnish (FIN) AF: 0.534 AC: 5646 AN: 10568

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33423 AN: 67938

Other (OTH) AF: 0.410 AC: 865 AN: 2108

Alfa AF: 0.459 Hom.: 24173

Bravo AF: 0.413

Asia WGS AF: 0.361 AC: 1256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.0
DANN	Benign	0.86
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs951436; hg19: chr1-163033342;