rs1058818

Variant names:

• chrY-18991654-C-T
• rs1058818
• ENST00000331787.3:n.373-58813G>A

Variant summary

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

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: CD24P4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 8 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=-0.76).

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.504-58813G>A		intron	N/A
	TTTY14	NR_125733.1		n.579-58179G>A		intron	N/A
	TTTY14	NR_125734.1		n.578+77070G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTTY14	ENST00000331787.3	TSL:1	n.373-58813G>A		intron	N/A
	TTTY14	ENST00000452584.5	TSL:3	n.335+52888G>A		intron	N/A
	TTTY14	ENST00000454875.3	TSL:2	n.448+85391G>A		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	-0.76
CADD	Benign	5.1
DANN	Benign	0.60
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1058818; hg19: chrY-21153540;