15-49720435-T-C

Variant names:

• chr15-49720435-T-C
• rs769136

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 0.173 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0631 AC: 2621 AN: 41568

American (AMR) AF: 0.205 AC: 3141 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1520 AN: 5184

South Asian (SAS) AF: 0.236 AC: 1141 AN: 4834

European-Finnish (FIN) AF: 0.131 AC: 1392 AN: 10602

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15153 AN: 68012

Other (OTH) AF: 0.195 AC: 413 AN: 2116

Alfa AF: 0.205 Hom.: 4331

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
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs769136; hg19: chr15-50012632;