rs1058881

Variant names:

• chrY-18991085-C-A
• rs1058881
• ENST00000331787.2:n.373-58244G>T

Your query was ambiguous. Multiple possible variants found:

• chrY-18991085-C-A
• chrY-18991085-C-T

Variant summary

Our verdict is Likely benign. Variant got -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: 0.0950

Genes affected

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

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD24P4		n.18991085C>A		intragenic_variant
TTTY14	NR_001543.4	n.504-58244G>T		intron_variant	Intron 1 of 1
TTTY14	NR_125733.1	n.579-57610G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTTY14	ENST00000331787.2	n.373-58244G>T		intron_variant	Intron 1 of 1	1
TTTY14	ENST00000452584.5	n.335+53457G>T		intron_variant	Intron 4 of 4	3
TTTY14	ENST00000454875.2	n.330+85960G>T		intron_variant	Intron 1 of 2	2

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1058881; hg19: chrY-21152971;