rs9786197

chrY-18956002-C-T

Variant summary

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

The NR_125735.1(TTTY14):n.504-78797G>A 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., 18419 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TTTY14 NR_125735.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

TTTY14 (HGNC:18495): (testis expressed transcript, Y-linked 14)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTTY14	NR_125735.1	n.504-78797G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTTY14	ENST00000651734.1	n.2240-78797G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 18341 AN: 31099 Hom.: 0 Cov.: 0 AF XY: 0.590 AC XY: 18341 AN XY: 31099 FAILED QC

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.956

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: 0.591 AC: 18419 AN: 31168 Hom.: 0 Cov.: 0 AF XY: 0.591 AC XY: 18419 AN XY: 31168

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.570

Alfa AF: 0.396 Hom.: 16617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9786197; hg19: chrY-21117888;