Y-15174113-T-C

Position:

• chrY-15174113-T-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., 18748 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15174113T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 18679 AN: 31986 Hom.: 0 Cov.: 0 AF XY: 0.584 AC XY: 18679 AN XY: 31986 FAILED QC

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.958

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.581

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: 0.585 AC: 18748 AN: 32047 Hom.: 0 Cov.: 0 AF XY: 0.585 AC XY: 18748 AN XY: 32047

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.589

Alfa AF: 0.397 Hom.: 16563

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17307398; hg19: chrY-17285993;