15-30003397-C-T

Variant names:

• chr15-30003397-C-T
• rs2140173

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 0.208 in 152,124 control chromosomes in the GnomAD database, including 3,683 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 0.21 (3683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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: 0.208 AC: 31651 AN: 152006 Hom.: 3683 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.208 AC: 31668 AN: 152124 Hom.: 3683 Cov.: 32 AF XY: 0.209 AC XY: 15508 AN XY: 74366

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.221

Alfa AF: 0.239 Hom.: 4283

Bravo AF: 0.203

Asia WGS AF: 0.285 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2140173; hg19: chr15-30295600;