15-49062185-T-C

Variant names:

• chr15-49062185-T-C
• rs935001

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 0.193 in 152,008 control chromosomes in the GnomAD database, including 3,275 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 0.19 (3275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.193 AC: 29389 AN: 151890 Hom.: 3273 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0947

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.193 AC: 29404 AN: 152008 Hom.: 3275 Cov.: 32 AF XY: 0.198 AC XY: 14732 AN XY: 74298

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.212

Alfa AF: 0.196 Hom.: 541

Bravo AF: 0.206

Asia WGS AF: 0.305 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.5
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: rs935001; hg19: chr15-49354382;