rs756656

Variant names:

• chr22-19592662-A-C
• rs756656

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;