chr15-22836312-G-A

Variant names:

• chr15-22836312-G-A
• rs7177395

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 0.191 in 152,042 control chromosomes in the GnomAD database, including 3,007 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 0.19 (3007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29040 AN: 151922 Hom.: 2999 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.191 AC: 29067 AN: 152042 Hom.: 3007 Cov.: 32 AF XY: 0.193 AC XY: 14342 AN XY: 74312

African (AFR) AF: 0.204 AC: 8453 AN: 41474

American (AMR) AF: 0.291 AC: 4445 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1706 AN: 5156

South Asian (SAS) AF: 0.180 AC: 867 AN: 4822

European-Finnish (FIN) AF: 0.158 AC: 1668 AN: 10560

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10578 AN: 67962

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.183 Hom.: 1837

Bravo AF: 0.201

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.91
DANN	Benign	0.53
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs7177395; hg19: chr15-23036756;