rs713756

chr22-44402430-G-Achr22-44402430-G-T

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 0.0813 in 152,282 control chromosomes in the GnomAD database, including 784 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 0.081 (784 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 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: 0.0813 AC: 12378 AN: 152164 Hom.: 784 Cov.: 33

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0813 AC: 12381 AN: 152282 Hom.: 784 Cov.: 33 AF XY: 0.0825 AC XY: 6142 AN XY: 74462

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0811

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0878

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0845 Hom.: 248

Bravo AF: 0.0832

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713756; hg19: chr22-44798310;