rs747226

Variant names:

• chr22-19747639-T-C
• rs747226

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 0.568 in 152,130 control chromosomes in the GnomAD database, including 24,617 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 0.57 (24617 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 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: 0.568 AC: 86338 AN: 152012 Hom.: 24594 Cov.: 34

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.568 AC: 86413 AN: 152130 Hom.: 24617 Cov.: 34 AF XY: 0.567 AC XY: 42181 AN XY: 74376

African (AFR) AF: 0.564 AC: 23428 AN: 41508

American (AMR) AF: 0.584 AC: 8942 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2320 AN: 3472

East Asian (EAS) AF: 0.586 AC: 3020 AN: 5150

South Asian (SAS) AF: 0.678 AC: 3272 AN: 4824

European-Finnish (FIN) AF: 0.485 AC: 5142 AN: 10598

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38537 AN: 67954

Other (OTH) AF: 0.564 AC: 1191 AN: 2110

Alfa AF: 0.581 Hom.: 30946

Bravo AF: 0.576

Asia WGS AF: 0.592 AC: 2057 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	0.23
DANN	Benign	0.43
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs747226; hg19: chr22-19735162; COSMIC: COSV60107260;