chr22-19747639-T-C

Position:

• chr22-19747639-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.564

Alfa AF: 0.581 Hom.: 26886

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

Splicing

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

Publications

LitVar

Other links and lift over

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