15-55602360-C-T

Variant names:

• chr15-55602360-C-T
• rs7175728

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 0.447 in 151,812 control chromosomes in the GnomAD database, including 16,256 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 0.45 (16256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 4 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 = 0.944 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67856 AN: 151694 Hom.: 16255 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.447 AC: 67870 AN: 151812 Hom.: 16256 Cov.: 32 AF XY: 0.459 AC XY: 34045 AN XY: 74206

African (AFR) AF: 0.456 AC: 18871 AN: 41410

American (AMR) AF: 0.448 AC: 6832 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3468

East Asian (EAS) AF: 0.966 AC: 4999 AN: 5174

South Asian (SAS) AF: 0.698 AC: 3357 AN: 4810

European-Finnish (FIN) AF: 0.432 AC: 4536 AN: 10512

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26212 AN: 67908

Other (OTH) AF: 0.422 AC: 885 AN: 2098

Alfa AF: 0.406 Hom.: 19303

Bravo AF: 0.444

Asia WGS AF: 0.765 AC: 2659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7175728; hg19: chr15-55894558;