Y-7779316-A-G

Position:

• chrY-7779316-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000651261.1(ENSG00000290323):​n.115-2612T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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., 17669 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ENST00000651261.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651261.1	n.115-2612T>C		intron_variant, non_coding_transcript_variant
	ENST00000442584.2	n.219-2288T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000652723.1	n.1027-2612T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 17609 AN: 30143 Hom.: 0 Cov.: 0 AF XY: 0.584 AC XY: 17609 AN XY: 30143 FAILED QC

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.562

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: 17669 AN: 30193 Hom.: 0 Cov.: 0 AF XY: 0.585 AC XY: 17669 AN XY: 30193

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.569

Alfa AF: 0.464 Hom.: 10876

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7067478; hg19: chrY-7647357;