15-62088060-C-T

Variant names:

• chr15-62088060-C-T
• rs7178424

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 0.421 in 152,050 control chromosomes in the GnomAD database, including 14,297 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 0.42 (14297 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64014 AN: 151932 Hom.: 14273 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.421 AC: 64081 AN: 152050 Hom.: 14297 Cov.: 33 AF XY: 0.430 AC XY: 31983 AN XY: 74346

African (AFR) AF: 0.308 AC: 12760 AN: 41434

American (AMR) AF: 0.527 AC: 8055 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2069 AN: 5176

South Asian (SAS) AF: 0.331 AC: 1595 AN: 4814

European-Finnish (FIN) AF: 0.672 AC: 7107 AN: 10578

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29867 AN: 67980

Other (OTH) AF: 0.427 AC: 900 AN: 2110

Alfa AF: 0.429 Hom.: 47880

Bravo AF: 0.409

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.57
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs7178424; hg19: chr15-62380259;