15-75157333-G-T

Variant names:

• chr15-75157333-G-T
• rs4886670

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 0.342 in 152,086 control chromosomes in the GnomAD database, including 12,084 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 0.34 (12084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• 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 = 0.655 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: 0.342 AC: 51911 AN: 151968 Hom.: 12051 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.342 AC: 51993 AN: 152086 Hom.: 12084 Cov.: 32 AF XY: 0.339 AC XY: 25219 AN XY: 74344

African (AFR) AF: 0.662 AC: 27449 AN: 41466

American (AMR) AF: 0.290 AC: 4436 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3472

East Asian (EAS) AF: 0.275 AC: 1419 AN: 5168

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10584

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13052 AN: 67984

Other (OTH) AF: 0.363 AC: 762 AN: 2102

Alfa AF: 0.258 Hom.: 9056

Bravo AF: 0.364

Asia WGS AF: 0.361 AC: 1254 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	3.8
DANN	Benign	0.85
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4886670; hg19: chr15-75449674;