chr15-37858237-C-T

Position:

• chr15-37858237-C-T

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 0.112 in 152,026 control chromosomes in the GnomAD database, including 1,175 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 0.11 (1175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16968 AN: 151906 Hom.: 1171 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.112 AC: 17001 AN: 152026 Hom.: 1175 Cov.: 32 AF XY: 0.115 AC XY: 8569 AN XY: 74308

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.0935

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0517

Gnomad4 NFE AF: 0.0729

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0832 Hom.: 796

Bravo AF: 0.121

Asia WGS AF: 0.139 AC: 483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	1.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8037309; hg19: chr15-38150438;