rs9662167

Positions:

• chr1-13625241-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;