chr15-75157333-G-T

Position:

• chr15-75157333-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 0.342 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.363

Alfa AF: 0.237 Hom.: 4987

Bravo AF: 0.364

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886670; hg19: chr15-75449674;