rs17149532

Variant names:

• chr7-126291328-T-G
• rs17149532

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 0.135 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0591 AC: 2457 AN: 41572

American (AMR) AF: 0.138 AC: 2104 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1228 AN: 5172

South Asian (SAS) AF: 0.189 AC: 913 AN: 4830

European-Finnish (FIN) AF: 0.195 AC: 2061 AN: 10582

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11016 AN: 68010

Other (OTH) AF: 0.128 AC: 271 AN: 2114

Alfa AF: 0.149 Hom.: 7089

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
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs17149532; hg19: chr7-125931382;