rs739161

Variant names:

• chr22-44349371-T-C
• rs739161

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.242 AC: 10039 AN: 41512

American (AMR) AF: 0.231 AC: 3531 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1629 AN: 5172

South Asian (SAS) AF: 0.198 AC: 955 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2892 AN: 10594

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19775 AN: 67974

Other (OTH) AF: 0.258 AC: 544 AN: 2110

Alfa AF: 0.280 Hom.: 9095

Bravo AF: 0.259

Asia WGS AF: 0.226 AC: 788 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs739161; hg19: chr22-44745251;