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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs4481791; hg19: chrY-21409706;