22-20674658-T-C

Variant names:

• chr22-20674658-T-C
• rs565979

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 0.54 in 151,988 control chromosomes in the GnomAD database, including 22,379 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 0.54 (22379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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: 0.540 AC: 82000 AN: 151870 Hom.: 22379 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.540 AC: 82038 AN: 151988 Hom.: 22379 Cov.: 32 AF XY: 0.547 AC XY: 40609 AN XY: 74296

African (AFR) AF: 0.480 AC: 19919 AN: 41470

American (AMR) AF: 0.488 AC: 7462 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1851 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2535 AN: 5176

South Asian (SAS) AF: 0.629 AC: 3030 AN: 4816

European-Finnish (FIN) AF: 0.714 AC: 7550 AN: 10568

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38039 AN: 67898

Other (OTH) AF: 0.517 AC: 1091 AN: 2110

Alfa AF: 0.557 Hom.: 17192

Bravo AF: 0.518

Asia WGS AF: 0.553 AC: 1925 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs565979; hg19: chr22-21028946;