15-96475503-C-T

Position:

• chr15-96475503-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 152,144 control chromosomes in the GnomAD database, including 1,245 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 (1245 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 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: 0.112 AC: 17040 AN: 152028 Hom.: 1247 Cov.: 31

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0211

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.112 AC: 17029 AN: 152144 Hom.: 1245 Cov.: 31 AF XY: 0.110 AC XY: 8159 AN XY: 74362

Gnomad4 AFR AF: 0.0289

Gnomad4 AMR AF: 0.0906

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0211

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.120

Alfa AF: 0.133 Hom.: 187

Bravo AF: 0.104

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113154706; hg19: chr15-97018733;