rs17011642

chr2-31853753-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 44 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00527

Gnomad4 AMR AF: 0.0246

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.0243

Gnomad4 NFE AF: 0.0297

Gnomad4 OTH AF: 0.0307

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17011642; hg19: chr2-32078822;