rs925646

Variant names:

• chr8-137492270-C-T
• rs925646

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 0.109 in 151,854 control chromosomes in the GnomAD database, including 1,153 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 0.11 (1153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 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: 0.109 AC: 16583 AN: 151740 Hom.: 1154 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.109 AC: 16576 AN: 151854 Hom.: 1153 Cov.: 32 AF XY: 0.116 AC XY: 8588 AN XY: 74182

African (AFR) AF: 0.0722 AC: 2994 AN: 41476

American (AMR) AF: 0.0981 AC: 1494 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1383 AN: 5146

South Asian (SAS) AF: 0.340 AC: 1629 AN: 4796

European-Finnish (FIN) AF: 0.112 AC: 1168 AN: 10464

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7282 AN: 67970

Other (OTH) AF: 0.104 AC: 220 AN: 2106

Alfa AF: 0.110 Hom.: 133

Bravo AF: 0.104

Asia WGS AF: 0.247 AC: 858 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0030
DANN	Benign	0.25
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs925646; hg19: chr8-138504513;