chr15-96883135-G-A

Position:

• chr15-96883135-G-A

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 0.221 in 152,036 control chromosomes in the GnomAD database, including 4,026 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 0.22 (4026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 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: 0.221 AC: 33646 AN: 151918 Hom.: 4028 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.221 AC: 33654 AN: 152036 Hom.: 4026 Cov.: 32 AF XY: 0.218 AC XY: 16176 AN XY: 74324

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.236

Alfa AF: 0.252 Hom.: 4154

Bravo AF: 0.219

Asia WGS AF: 0.170 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs983188; hg19: chr15-97426365;