rs9785959

Positions:

• chrY-15670298-G-C

Variant summary

Our verdict is Likely benign. Variant got -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 0.59 (0 hom., 18879 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 18807 AN: 31760 Hom.: 0 Cov.: 0 AF XY: 0.592 AC XY: 18807 AN XY: 31760 FAILED QC

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.970

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.568

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: 0.593 AC: 18879 AN: 31823 Hom.: 0 Cov.: 0 AF XY: 0.593 AC XY: 18879 AN XY: 31823

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.576

Alfa AF: 0.345 Hom.: 205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.56
DANN	Benign	0.094

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9785959; hg19: chrY-17782178;