rs756656

Positions:

• chr22-19592662-A-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 0.634 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.566

Alfa AF: 0.557 Hom.: 48297

Bravo AF: 0.636

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs756656; hg19: chr22-19580185;