22-20197488-T-C

Variant names:

• chr22-20197488-T-C
• rs665780

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 0.258 in 151,972 control chromosomes in the GnomAD database, including 5,545 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 0.26 (5545 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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: 0.258 AC: 39161 AN: 151854 Hom.: 5534 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.258 AC: 39193 AN: 151972 Hom.: 5545 Cov.: 32 AF XY: 0.261 AC XY: 19354 AN XY: 74282

African (AFR) AF: 0.370 AC: 15338 AN: 41406

American (AMR) AF: 0.209 AC: 3197 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1730 AN: 5142

South Asian (SAS) AF: 0.199 AC: 960 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2622 AN: 10580

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13586 AN: 67946

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.236 Hom.: 599

Bravo AF: 0.264

Asia WGS AF: 0.251 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.016
DANN	Benign	0.57
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs665780; hg19: chr22-20185011;