Y-13221267-T-C

Position:

• chrY-13221267-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 0.95 (0 hom., 31091 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13221267T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 31027 AN: 32495 Hom.: 0 Cov.: 0 AF XY: 0.955 AC XY: 31027 AN XY: 32495 FAILED QC

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.943

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: 0.955 AC: 31091 AN: 32559 Hom.: 0 Cov.: 0 AF XY: 0.955 AC XY: 31091 AN XY: 32559

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.975

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.925

Gnomad4 OTH AF: 0.943

Alfa AF: 0.907 Hom.: 32001

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1236440; hg19: chrY-15333149;