chrY-18956002-C-T

Variant names:

• chrY-18956002-C-T
• rs9786197
• ENST00000331787.3:n.373-23161G>A

Variant summary

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

The ENST00000331787.3(TTTY14):​n.373-23161G>A 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., 18419 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TTTY14 ENST00000331787.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000331787.3. 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
	TTTY14	NR_001543.4		n.504-23161G>A		intron	N/A
	TTTY14	NR_125733.1		n.579-22527G>A		intron	N/A
	TTTY14	NR_125734.1		n.579-78797G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTTY14	ENST00000331787.3	TSL:1	n.373-23161G>A		intron	N/A
	TTTY14	ENST00000452584.5	TSL:3	n.336-23161G>A		intron	N/A
	TTTY14	ENST00000454875.3	TSL:2	n.449-78797G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.590 AC: 18341 AN: 31099 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.793 AC: 6250 AN: 7878

American (AMR) AF: 0.502 AC: 1681 AN: 3347

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 597 AN: 736

East Asian (EAS) AF: 0.996 AC: 1154 AN: 1159

South Asian (SAS) AF: 0.663 AC: 893 AN: 1347

European-Finnish (FIN) AF: 0.935 AC: 2748 AN: 2940

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

European-Non Finnish (NFE) AF: 0.362 AC: 4730 AN: 13050

Other (OTH) AF: 0.570 AC: 249 AN: 437

Alfa AF: 0.450 Hom.: 27659

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9786197; hg19: chrY-21117888;