rs9785959

Variant names:

• chrY-15670298-G-C
• rs9785959

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 0.59 (0 hom., 18879 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 5 publications found

ACMG classification

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

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

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: 0.592 AC: 18807 AN: 31760 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.793 AC: 6409 AN: 8081

American (AMR) AF: 0.507 AC: 1741 AN: 3432

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 607 AN: 749

East Asian (EAS) AF: 0.996 AC: 1137 AN: 1142

South Asian (SAS) AF: 0.650 AC: 923 AN: 1421

European-Finnish (FIN) AF: 0.934 AC: 2874 AN: 3077

Middle Eastern (MID) AF: 0.969 AC: 63 AN: 65

European-Non Finnish (NFE) AF: 0.365 AC: 4822 AN: 13215

Other (OTH) AF: 0.576 AC: 251 AN: 436

Alfa AF: 0.345 Hom.: 205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.56
DANN	Benign	0.094
PhyloP100		-0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9785959;

hg19: chrY-17782178;