rs9662167

Variant names:

• chr1-13625241-C-T
• rs9662167

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 0.407 in 151,426 control chromosomes in the GnomAD database, including 13,197 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 0.41 (13197 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 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: 0.407 AC: 61595 AN: 151308 Hom.: 13198 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.407 AC: 61604 AN: 151426 Hom.: 13197 Cov.: 31 AF XY: 0.402 AC XY: 29715 AN XY: 73918

African (AFR) AF: 0.280 AC: 11586 AN: 41308

American (AMR) AF: 0.499 AC: 7602 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1626 AN: 3462

East Asian (EAS) AF: 0.325 AC: 1676 AN: 5150

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4806

European-Finnish (FIN) AF: 0.398 AC: 4124 AN: 10354

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32051 AN: 67824

Other (OTH) AF: 0.431 AC: 906 AN: 2100

Alfa AF: 0.442 Hom.: 1901

Bravo AF: 0.415

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs9662167; hg19: chr1-13951736;