ENST00000331787.3:n.373-59119T>G

Variant names:

• chrY-18991960-A-C
• rs4030414
• ENST00000331787.3:n.373-59119T>G

Variant summary

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

The ENST00000331787.3(TTTY14):​n.373-59119T>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: not found (cov: 0)
• Consequence: TTTY14 ENST00000331787.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 1 publications found

Genes affected

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

CD24P4 (HGNC:1649): (CD24 molecule pseudogene 4)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).

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.504-59119T>G		intron	N/A
	TTTY14	NR_125733.1		n.579-58485T>G		intron	N/A
	TTTY14	NR_125734.1		n.578+76764T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTTY14	ENST00000331787.3	TSL:1	n.373-59119T>G		intron	N/A
	TTTY14	ENST00000452584.5	TSL:3	n.335+52582T>G		intron	N/A
	TTTY14	ENST00000454875.3	TSL:2	n.448+85085T>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4030414; hg19: chrY-21153846;