rs17149532

Variant names:

• chr7-126291328-T-G
• rs17149532

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 0.135 in 152,246 control chromosomes in the GnomAD database, including 1,629 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 0.14 (1629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 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: 0.135 AC: 20609 AN: 152128 Hom.: 1631 Cov.: 32

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.135 AC: 20609 AN: 152246 Hom.: 1629 Cov.: 32 AF XY: 0.141 AC XY: 10510 AN XY: 74422

Gnomad4 AFR AF: 0.0591

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.128

Alfa AF: 0.154 Hom.: 3661

Bravo AF: 0.124

Asia WGS AF: 0.204 AC: 707 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17149532; hg19: chr7-125931382;