chr22-20379205-T-G

Variant names:

• chr22-20379205-T-G
• rs6003971

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 0.182 in 152,164 control chromosomes in the GnomAD database, including 4,181 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 0.18 (4181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 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: 0.182 AC: 27668 AN: 152046 Hom.: 4178 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0940

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.182 AC: 27692 AN: 152164 Hom.: 4181 Cov.: 32 AF XY: 0.177 AC XY: 13138 AN XY: 74400

African (AFR) AF: 0.418 AC: 17316 AN: 41460

American (AMR) AF: 0.119 AC: 1822 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3468

East Asian (EAS) AF: 0.00578 AC: 30 AN: 5188

South Asian (SAS) AF: 0.0603 AC: 291 AN: 4826

European-Finnish (FIN) AF: 0.0867 AC: 919 AN: 10596

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0940 AC: 6393 AN: 68020

Other (OTH) AF: 0.156 AC: 329 AN: 2114

Alfa AF: 0.109 Hom.: 1815

Bravo AF: 0.193

Asia WGS AF: 0.0610 AC: 215 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		-0.084

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6003971; hg19: chr22-20733495;