Y-19247820-C-G

Variant names:

• chrY-19247820-C-G
• rs4481791

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 0.58 (0 hom., 17426 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.580 AC: 17385 AN: 29978 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.569

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: 0.581 AC: 17426 AN: 30012 Hom.: 0 Cov.: 0 AF XY: 0.581 AC XY: 17426 AN XY: 30012

African (AFR) AF: 0.791 AC: 6002 AN: 7587

American (AMR) AF: 0.501 AC: 1612 AN: 3216

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 585 AN: 724

East Asian (EAS) AF: 0.996 AC: 1116 AN: 1120

South Asian (SAS) AF: 0.515 AC: 674 AN: 1309

European-Finnish (FIN) AF: 0.934 AC: 2504 AN: 2682

Middle Eastern (MID) AF: 0.957 AC: 66 AN: 69

European-Non Finnish (NFE) AF: 0.361 AC: 4573 AN: 12683

Other (OTH) AF: 0.574 AC: 236 AN: 411

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.78
DANN	Benign	0.38
PhyloP100		-2.3

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: rs4481791;

hg19: chrY-21409706;