rs17882950

Positions:

• chr22-35378927-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.00782

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.00518

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0616

Gnomad4 NFE AF: 0.0408

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0396 Hom.: 24

Bravo AF: 0.0396

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17882950; hg19: chr22-35774920;