rs6746899
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_110252.1(LOC101929452):n.343-283T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,218 control chromosomes in the GnomAD database, including 1,445 homozygotes. 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: 𝑓 0.14 ( 1445 hom., cov: 32)
Consequence
LOC101929452
NR_110252.1 intron, non_coding_transcript
NR_110252.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.323
Genes affected
RNF144A (HGNC:20457): (ring finger protein 144A) This gene encodes a member of a family of RING finger domain-containing E3 ubiquitin ligases that also includes parkin and parc. The expression of this gene is induced by DNA damage. The encoded protein interacts with the cytoplasmic DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) and promotes its degradation through ubiquitination. The orthologous mouse protein has been shown to interact with a ubiquitin-conjugating enzyme involved in embryonic development. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC101929452 | NR_110252.1 | n.343-283T>C | intron_variant, non_coding_transcript_variant | ||||
RNF144A | NM_001349181.2 | c.748-9965A>G | intron_variant | ||||
RNF144A | NM_001349185.2 | c.748-5019A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000664324.1 | n.711+13685T>C | intron_variant, non_coding_transcript_variant | |||||||
RNF144A | ENST00000432850.1 | c.735-5019A>G | intron_variant | 3 | |||||
ENST00000415520.5 | n.343-283T>C | intron_variant, non_coding_transcript_variant | 4 | ||||||
ENST00000649356.2 | n.1010-283T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.135 AC: 20551AN: 152100Hom.: 1442 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.135 AC: 20564AN: 152218Hom.: 1445 Cov.: 32 AF XY: 0.138 AC XY: 10255AN XY: 74424
GnomAD4 genome
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369
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at