15-54918507-C-T

Variant names:

• chr15-54918507-C-T
• rs1528460

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 0.538 in 152,122 control chromosomes in the GnomAD database, including 26,508 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 0.54 (26508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 15 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 (NFE) allele frequency at 95% confidence interval = 0.694 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: 0.539 AC: 81881 AN: 152004 Hom.: 26516 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.538 AC: 81872 AN: 152122 Hom.: 26508 Cov.: 32 AF XY: 0.544 AC XY: 40448 AN XY: 74358

African (AFR) AF: 0.155 AC: 6445 AN: 41510

American (AMR) AF: 0.610 AC: 9334 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2366 AN: 3472

East Asian (EAS) AF: 0.608 AC: 3132 AN: 5152

South Asian (SAS) AF: 0.599 AC: 2890 AN: 4824

European-Finnish (FIN) AF: 0.785 AC: 8300 AN: 10578

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47540 AN: 67982

Other (OTH) AF: 0.577 AC: 1218 AN: 2110

Alfa AF: 0.649 Hom.: 107561

Bravo AF: 0.510

Asia WGS AF: 0.543 AC: 1886 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	7.4
DANN	Benign	0.40
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1528460; hg19: chr15-55210705;