Y-9332936-A-C

Variant names:

• chrY-9332936-A-C
• rs9786194
• ENST00000434487.1:n.82+1815T>G

Variant summary

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

The ENST00000434487.1(TTTY20):​n.82+1815T>G 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 0.65 (0 hom., 20842 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TTTY20 ENST00000434487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTTY20	NR_001546.1	n.82+1815T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTTY20	ENST00000434487.1	n.82+1815T>G		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 20773 AN: 31791 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.803 AC: 6508 AN: 8101

American (AMR) AF: 0.499 AC: 1751 AN: 3508

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 674 AN: 756

East Asian (EAS) AF: 0.999 AC: 1191 AN: 1192

South Asian (SAS) AF: 0.982 AC: 1330 AN: 1355

European-Finnish (FIN) AF: 0.975 AC: 2998 AN: 3075

Middle Eastern (MID) AF: 0.985 AC: 65 AN: 66

European-Non Finnish (NFE) AF: 0.456 AC: 5995 AN: 13154

Other (OTH) AF: 0.626 AC: 271 AN: 433

Alfa AF: 0.515 Hom.: 18044

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs9786194; hg19: chrY-9170545;