rs891407

Variant names:

• chrY-19681204-G-C
• rs891407

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., 19485 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• 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=-0.91).

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: 0.590 AC: 19412 AN: 32911 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.566

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: 0.591 AC: 19485 AN: 32977 Hom.: 0 Cov.: 0 AF XY: 0.591 AC XY: 19485 AN XY: 32977

African (AFR) AF: 0.794 AC: 6672 AN: 8399

American (AMR) AF: 0.503 AC: 1859 AN: 3694

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 602 AN: 752

East Asian (EAS) AF: 0.996 AC: 1190 AN: 1195

South Asian (SAS) AF: 0.535 AC: 774 AN: 1448

European-Finnish (FIN) AF: 0.935 AC: 3123 AN: 3340

Middle Eastern (MID) AF: 0.958 AC: 69 AN: 72

European-Non Finnish (NFE) AF: 0.364 AC: 4878 AN: 13406

Other (OTH) AF: 0.574 AC: 265 AN: 462

Alfa AF: 0.394 Hom.: 5153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.29
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs891407; hg19: chrY-21843090;