rs17250932

Variant names:

• chr17-47731941-T-C
• rs17250932

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 0.162 in 152,082 control chromosomes in the GnomAD database, including 2,116 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 0.16 (2116 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 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: 0.162 AC: 24672 AN: 151964 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.162 AC: 24673 AN: 152082 Hom.: 2116 Cov.: 32 AF XY: 0.165 AC XY: 12262 AN XY: 74306

African (AFR) AF: 0.123 AC: 5084 AN: 41480

American (AMR) AF: 0.200 AC: 3062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.0672 AC: 348 AN: 5182

South Asian (SAS) AF: 0.188 AC: 902 AN: 4808

European-Finnish (FIN) AF: 0.225 AC: 2376 AN: 10558

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11879 AN: 67986

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.166 Hom.: 2817

Bravo AF: 0.161

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs17250932; hg19: chr17-45809307;