rs739161

Variant names:

• chr22-44349371-T-C
• rs739161

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 0.265 in 152,154 control chromosomes in the GnomAD database, including 5,498 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 0.27 (5498 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.265 AC: 40310 AN: 152036 Hom.: 5492 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.265 AC: 40337 AN: 152154 Hom.: 5498 Cov.: 33 AF XY: 0.262 AC XY: 19494 AN XY: 74388

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.258

Alfa AF: 0.270 Hom.: 1022

Bravo AF: 0.259

Asia WGS AF: 0.226 AC: 788 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
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: rs739161; hg19: chr22-44745251;