rs17882950

Variant names:

• chr22-35378927-C-T
• rs17882950

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 0.0376 in 152,296 control chromosomes in the GnomAD database, including 217 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 0.038 (217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 5719 AN: 152178 Hom.: 214 Cov.: 32

Gnomad AFR AF: 0.00784

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0376 AC: 5723 AN: 152296 Hom.: 217 Cov.: 32 AF XY: 0.0394 AC XY: 2934 AN XY: 74474

African (AFR) AF: 0.00782 AC: 325 AN: 41552

American (AMR) AF: 0.117 AC: 1784 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00518 AC: 18 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4830

European-Finnish (FIN) AF: 0.0616 AC: 654 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0408 AC: 2776 AN: 68020

Other (OTH) AF: 0.0303 AC: 64 AN: 2114

Alfa AF: 0.0360 Hom.: 46

Bravo AF: 0.0396

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.73
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs17882950; hg19: chr22-35774920;