rs52812045

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000382840.3(CD24P4):​n.170C>T variant causes a non coding transcript exon 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

CD24P4
ENST00000382840.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.647
Variant links:
Genes affected
CD24P4 (HGNC:1649): (CD24 molecule pseudogene 4)
TTTY14 (HGNC:18495): (testis expressed transcript, Y-linked 14)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TTTY14NR_125735.1 linkuse as main transcriptn.503+84505C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD24P4ENST00000382840.3 linkuse as main transcriptn.170C>T non_coding_transcript_exon_variant 1/1
TTTY14ENST00000651734.1 linkuse as main transcriptn.2239+48830C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.188
Hom.:
206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.5
DANN
Benign
0.73

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs52812045; hg19: chrY-21154426; API