15-62099409-C-T

Variant names:

• chr15-62099409-C-T
• rs7163757

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.506 in 151,990 control chromosomes in the GnomAD database, including 20,530 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 0.51 (20530 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.505 AC: 76767 AN: 151872 Hom.: 20470 Cov.: 33

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.506 AC: 76897 AN: 151990 Hom.: 20530 Cov.: 33 AF XY: 0.507 AC XY: 37683 AN XY: 74290

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.494

Alfa AF: 0.430 Hom.: 23507

Bravo AF: 0.508

Asia WGS AF: 0.443 AC: 1537 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7163757; hg19: chr15-62391608;