Y-18991960-A-G

Variant names:

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

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>C 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=-0.48).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD24P4		n.18991960A>G		intragenic_variant
TTTY14	NR_001543.4	n.504-59119T>C		intron_variant	Intron 1 of 1
TTTY14	NR_125733.1	n.579-58485T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTTY14	ENST00000331787.3	n.373-59119T>C		intron_variant	Intron 1 of 1	1
TTTY14	ENST00000452584.5	n.335+52582T>C		intron_variant	Intron 4 of 4	3
TTTY14	ENST00000454875.3	n.448+85085T>C		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	-0.48
CADD	Benign	1.2
DANN	Benign	0.62
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;