Y-15732138-C-T

Variant names:

• chrY-15732138-C-T
• rs9786076

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.67 (0 hom., 21717 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 7 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

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: 0.671 AC: 21646 AN: 32251 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.985

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.612

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.672 AC: 21717 AN: 32317 Hom.: 0 Cov.: 0 AF XY: 0.672 AC XY: 21717 AN XY: 32317

African (AFR) AF: 0.815 AC: 6708 AN: 8226

American (AMR) AF: 0.534 AC: 1887 AN: 3533

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 722 AN: 764

East Asian (EAS) AF: 1.00 AC: 1179 AN: 1179

South Asian (SAS) AF: 1.00 AC: 1368 AN: 1368

European-Finnish (FIN) AF: 0.974 AC: 3103 AN: 3187

Middle Eastern (MID) AF: 0.985 AC: 66 AN: 67

European-Non Finnish (NFE) AF: 0.476 AC: 6349 AN: 13334

Other (OTH) AF: 0.615 AC: 275 AN: 447

Alfa AF: 0.542 Hom.: 31039

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.2
DANN	Benign	0.37
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs9786076; hg19: chrY-17844018;