chr15-101267710-T-C

Position:

• chr15-101267710-T-C

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 0.192 in 152,202 control chromosomes in the GnomAD database, including 3,647 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 (3647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29217 AN: 152086 Hom.: 3646 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.192 AC: 29221 AN: 152202 Hom.: 3647 Cov.: 32 AF XY: 0.194 AC XY: 14440 AN XY: 74402

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.183

Alfa AF: 0.229 Hom.: 5747

Bravo AF: 0.178

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2101171; hg19: chr15-101807915;