15-37338164-T-C

Variant names:

• chr15-37338164-T-C
• rs4924148

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 0.265 in 150,890 control chromosomes in the GnomAD database, including 5,684 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 0.27 (5684 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 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: 0.265 AC: 40024 AN: 150780 Hom.: 5690 Cov.: 29

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.265 AC: 40019 AN: 150890 Hom.: 5684 Cov.: 29 AF XY: 0.263 AC XY: 19349 AN XY: 73630

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.277

Alfa AF: 0.318 Hom.: 16485

Bravo AF: 0.259

Asia WGS AF: 0.152 AC: 528 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.60
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4924148; hg19: chr15-37630365;