15-49720435-T-C

Variant names:

• chr15-49720435-T-C
• rs769136

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 0.173 in 152,296 control chromosomes in the GnomAD database, including 2,759 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 0.17 (2759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.173 AC: 26383 AN: 152178 Hom.: 2757 Cov.: 32

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.173 AC: 26383 AN: 152296 Hom.: 2759 Cov.: 32 AF XY: 0.172 AC XY: 12842 AN XY: 74474

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.195

Alfa AF: 0.210 Hom.: 3552

Bravo AF: 0.175

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs769136; hg19: chr15-50012632;