rs9662167

Variant names:

• chr1-13625241-C-T
• rs9662167

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 0.407 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.431

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9662167; hg19: chr1-13951736;