rs17011642

Variant names:

• chr2-31853753-T-G
• rs17011642

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0215 in 152,250 control chromosomes in the GnomAD database, including 44 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 0.022 (44 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0215 (3280/152250) while in subpopulation SAS AF = 0.0421 (203/4822). AF 95% confidence interval is 0.0374. There are 44 homozygotes in GnomAd4. There are 1624 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 gene

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: 0.0216 AC: 3281 AN: 152132 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00529

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0243

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.0310

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

GnomAD4 genome AF: 0.0215 AC: 3280 AN: 152250 Hom.: 44 Cov.: 32 AF XY: 0.0218 AC XY: 1624 AN XY: 74448

African (AFR) AF: 0.00527 AC: 219 AN: 41550

American (AMR) AF: 0.0246 AC: 377 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4822

European-Finnish (FIN) AF: 0.0243 AC: 257 AN: 10588

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0297 AC: 2022 AN: 68014

Other (OTH) AF: 0.0307 AC: 65 AN: 2116

Alfa AF: 0.0224 Hom.: 3

Bravo AF: 0.0208

Asia WGS AF: 0.0150 AC: 51 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	0.33
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs17011642; hg19: chr2-32078822;