rs9674875

Variant names:

• chr17-10227528-G-A
• rs9674875

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 0.435 in 151,826 control chromosomes in the GnomAD database, including 16,223 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 0.43 (16223 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 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: 0.435 AC: 65951 AN: 151708 Hom.: 16188 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.435 AC: 66044 AN: 151826 Hom.: 16223 Cov.: 31 AF XY: 0.431 AC XY: 31995 AN XY: 74216

African (AFR) AF: 0.675 AC: 27932 AN: 41390

American (AMR) AF: 0.468 AC: 7139 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3460

East Asian (EAS) AF: 0.370 AC: 1901 AN: 5142

South Asian (SAS) AF: 0.309 AC: 1490 AN: 4822

European-Finnish (FIN) AF: 0.300 AC: 3164 AN: 10546

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22277 AN: 67906

Other (OTH) AF: 0.414 AC: 874 AN: 2110

Alfa AF: 0.372 Hom.: 31846

Bravo AF: 0.460

Asia WGS AF: 0.339 AC: 1176 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.69
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9674875; hg19: chr17-10130845;