chr22-19592662-A-C

Variant names:

• chr22-19592662-A-C
• rs756656

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 0.634 in 152,062 control chromosomes in the GnomAD database, including 31,714 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 0.63 (31714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96303 AN: 151944 Hom.: 31651 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.634 AC: 96426 AN: 152062 Hom.: 31714 Cov.: 32 AF XY: 0.633 AC XY: 47087 AN XY: 74332

African (AFR) AF: 0.836 AC: 34675 AN: 41486

American (AMR) AF: 0.550 AC: 8403 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1801 AN: 3466

East Asian (EAS) AF: 0.589 AC: 3047 AN: 5170

South Asian (SAS) AF: 0.580 AC: 2796 AN: 4820

European-Finnish (FIN) AF: 0.608 AC: 6420 AN: 10554

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37342 AN: 67980

Other (OTH) AF: 0.566 AC: 1196 AN: 2114

Alfa AF: 0.575 Hom.: 81176

Bravo AF: 0.636

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.73
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs756656; hg19: chr22-19580185;