rs7169523

Positions:

• chr15-31171175-G-A
• chr15-31171175-G-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 0.202 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.205

Alfa AF: 0.221 Hom.: 3544

Bravo AF: 0.196

Asia WGS AF: 0.410 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7169523; hg19: chr15-31463378;