15-31171175-G-A

Variant names:

• chr15-31171175-G-A
• rs7169523

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 0.202 in 152,152 control chromosomes in the GnomAD database, including 4,104 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 0.20 (4104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.202 AC: 30671 AN: 152034 Hom.: 4102 Cov.: 32

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.202 AC: 30665 AN: 152152 Hom.: 4104 Cov.: 32 AF XY: 0.208 AC XY: 15476 AN XY: 74382

African (AFR) AF: 0.0674 AC: 2800 AN: 41542

American (AMR) AF: 0.215 AC: 3293 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3357 AN: 5144

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4824

European-Finnish (FIN) AF: 0.243 AC: 2571 AN: 10588

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15364 AN: 67968

Other (OTH) AF: 0.205 AC: 434 AN: 2112

Alfa AF: 0.207 Hom.: 6296

Bravo AF: 0.196

Asia WGS AF: 0.410 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.21
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs7169523; hg19: chr15-31463378;