15-93209649-T-C

Variant names:

• chr15-93209649-T-C
• rs1872052

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 0.445 in 152,084 control chromosomes in the GnomAD database, including 15,733 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 0.44 (15733 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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: 0.445 AC: 67657 AN: 151966 Hom.: 15729 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.445 AC: 67676 AN: 152084 Hom.: 15733 Cov.: 33 AF XY: 0.446 AC XY: 33160 AN XY: 74344

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.427

Alfa AF: 0.484 Hom.: 37584

Bravo AF: 0.425

Asia WGS AF: 0.515 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872052; hg19: chr15-93752878;