rs9786194

chrY-9332936-A-CchrY-9332936-A-T

Variant summary

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

The NR_001546.1(TTTY20):n.82+1815T>G 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 0.65 (0 hom., 20842 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TTTY20 NR_001546.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

TTTY20 (HGNC:18844): (testis expressed transcript, Y-linked 20)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTTY20	NR_001546.1	n.82+1815T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTTY20	ENST00000434487.1	n.82+1815T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 20773 AN: 31791 Hom.: 0 Cov.: 0 AF XY: 0.653 AC XY: 20773 AN XY: 31791 FAILED QC

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.985

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.619

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: 0.654 AC: 20842 AN: 31851 Hom.: 0 Cov.: 0 AF XY: 0.654 AC XY: 20842 AN XY: 31851

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.982

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.626

Alfa AF: 0.463 Hom.: 9822

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.79
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9786194; hg19: chrY-9170545;