chr7-15591246-A-G

Variant names:

• chr7-15591246-A-G
• rs11763353

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 0.208 in 152,098 control chromosomes in the GnomAD database, including 4,449 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 0.21 (4449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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: 0.208 AC: 31649 AN: 151980 Hom.: 4441 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.208 AC: 31691 AN: 152098 Hom.: 4449 Cov.: 32 AF XY: 0.207 AC XY: 15380 AN XY: 74356

African (AFR) AF: 0.399 AC: 16535 AN: 41470

American (AMR) AF: 0.126 AC: 1932 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5168

South Asian (SAS) AF: 0.109 AC: 526 AN: 4824

European-Finnish (FIN) AF: 0.225 AC: 2374 AN: 10572

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9347 AN: 67992

Other (OTH) AF: 0.187 AC: 396 AN: 2114

Alfa AF: 0.155 Hom.: 1170

Bravo AF: 0.208

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.93
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11763353; hg19: chr7-15630871;