15-45344386-C-T

Variant names:

• chr15-45344386-C-T
• rs1153860

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 0.56 in 152,138 control chromosomes in the GnomAD database, including 27,366 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 0.56 (27366 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.560 AC: 85115 AN: 152020 Hom.: 27311 Cov.: 33

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.560 AC: 85233 AN: 152138 Hom.: 27366 Cov.: 33 AF XY: 0.567 AC XY: 42180 AN XY: 74396

African (AFR) AF: 0.841 AC: 34913 AN: 41522

American (AMR) AF: 0.620 AC: 9472 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1854 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4704 AN: 5182

South Asian (SAS) AF: 0.592 AC: 2856 AN: 4826

European-Finnish (FIN) AF: 0.409 AC: 4328 AN: 10576

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25542 AN: 67962

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.474 Hom.: 21920

Bravo AF: 0.592

Asia WGS AF: 0.736 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.021
DANN	Benign	0.21
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1153860; hg19: chr15-45636584;