rs9786232

Variant names:

• chrY-19004472-G-T
• rs9786232
• ENST00000331787.3:n.373-71631C>A

Variant summary

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

The ENST00000331787.3(TTTY14):​n.373-71631C>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., 18350 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TTTY14 ENST00000331787.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• 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=-1.02).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTTY14	NR_001543.4		n.504-71631C>A		intron	N/A
	TTTY14	NR_125733.1		n.578+64252C>A		intron	N/A
	TTTY14	NR_125734.1		n.578+64252C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTTY14	ENST00000331787.3	TSL:1	n.373-71631C>A		intron	N/A
	TTTY14	ENST00000452584.5	TSL:3	n.335+40070C>A		intron	N/A
	TTTY14	ENST00000454875.3	TSL:2	n.448+72573C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.589 AC: 18284 AN: 31039 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.564

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: 0.590 AC: 18350 AN: 31096 Hom.: 0 Cov.: 0 AF XY: 0.590 AC XY: 18350 AN XY: 31096

African (AFR) AF: 0.794 AC: 6181 AN: 7786

American (AMR) AF: 0.497 AC: 1669 AN: 3358

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 595 AN: 735

East Asian (EAS) AF: 0.997 AC: 1162 AN: 1166

South Asian (SAS) AF: 0.649 AC: 867 AN: 1335

European-Finnish (FIN) AF: 0.932 AC: 2735 AN: 2933

Middle Eastern (MID) AF: 0.972 AC: 69 AN: 71

European-Non Finnish (NFE) AF: 0.365 AC: 4770 AN: 13073

Other (OTH) AF: 0.571 AC: 248 AN: 434

Alfa AF: 0.441 Hom.: 23357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.18
PhyloP100		-0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9786232;

hg19: chrY-21166358;