15-91045317-T-C

Variant names:

• chr15-91045317-T-C
• rs1005060

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.409 in 151,980 control chromosomes in the GnomAD database, including 14,142 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 0.41 (14142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 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: 0.409 AC: 62105 AN: 151862 Hom.: 14141 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.409 AC: 62119 AN: 151980 Hom.: 14142 Cov.: 32 AF XY: 0.417 AC XY: 30988 AN XY: 74286

African (AFR) AF: 0.239 AC: 9888 AN: 41458

American (AMR) AF: 0.546 AC: 8341 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3470

East Asian (EAS) AF: 0.849 AC: 4387 AN: 5170

South Asian (SAS) AF: 0.561 AC: 2695 AN: 4808

European-Finnish (FIN) AF: 0.435 AC: 4582 AN: 10538

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29404 AN: 67958

Other (OTH) AF: 0.432 AC: 912 AN: 2112

Alfa AF: 0.432 Hom.: 50165

Bravo AF: 0.407

Asia WGS AF: 0.662 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.46
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1005060; hg19: chr15-91588547;