15-99495231-C-G

Variant names:

• chr15-99495231-C-G
• rs7181055

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 0.245 in 152,188 control chromosomes in the GnomAD database, including 5,075 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 0.25 (5075 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.245 AC: 37333 AN: 152070 Hom.: 5081 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.245 AC: 37332 AN: 152188 Hom.: 5075 Cov.: 33 AF XY: 0.252 AC XY: 18782 AN XY: 74396

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.226

Alfa AF: 0.0579 Hom.: 63

Bravo AF: 0.243

Asia WGS AF: 0.486 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7181055; hg19: chr15-100035436;