Y-7779316-A-G

Variant names:

• chrY-7779316-A-G
• rs7067478
• ENST00000442584.2:n.219-2288T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000442584.2(TTTY16):​n.219-2288T>C variant causes a intron 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: TTTY16 ENST00000442584.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 4 publications found

Genes affected

TTTY16 (HGNC:18840): (testis expressed transcript, Y-linked 16)

LOC107987339 (HGNC:):

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442584.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTTY16	ENST00000442584.2	TSL:5	n.219-2288T>C		intron	N/A
	TTTY16	ENST00000651261.1		n.115-2612T>C		intron	N/A
	TTTY16	ENST00000652723.1		n.1027-2612T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.584 AC: 17609 AN: 30143 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.793 AC: 6089 AN: 7678

American (AMR) AF: 0.497 AC: 1615 AN: 3250

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 589 AN: 733

East Asian (EAS) AF: 0.996 AC: 1132 AN: 1136

South Asian (SAS) AF: 0.655 AC: 873 AN: 1333

European-Finnish (FIN) AF: 0.926 AC: 2381 AN: 2570

Middle Eastern (MID) AF: 0.956 AC: 65 AN: 68

European-Non Finnish (NFE) AF: 0.362 AC: 4635 AN: 12809

Other (OTH) AF: 0.569 AC: 234 AN: 411

Alfa AF: 0.500 Hom.: 18553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.34
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7067478; hg19: chrY-7647357;