rs5756381

Positions:

• chr22-36881574-A-G
• chr22-36881574-A-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 0.688 in 152,080 control chromosomes in the GnomAD database, including 36,620 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 0.69 (36620 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 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: 0.689 AC: 104640 AN: 151962 Hom.: 36600 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.688 AC: 104703 AN: 152080 Hom.: 36620 Cov.: 33 AF XY: 0.693 AC XY: 51529 AN XY: 74344

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.696

Alfa AF: 0.704 Hom.: 5538

Bravo AF: 0.679

Asia WGS AF: 0.730 AC: 2534 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
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: rs5756381; hg19: chr22-37277616;