chr12-47716542-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001172439.2(ENDOU):c.552-43T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.96 in 1,595,668 control chromosomes in the GnomAD database, including 735,476 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. There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_001172439.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENDOU | NM_001172439.2 | c.552-43T>C | intron_variant | ENST00000422538.8 | |||
RPAP3-DT | NR_183480.1 | n.77-2605A>G | intron_variant, non_coding_transcript_variant | ||||
ENDOU | NM_001172440.2 | c.363-43T>C | intron_variant | ||||
ENDOU | NM_006025.4 | c.429-43T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENDOU | ENST00000422538.8 | c.552-43T>C | intron_variant | 1 | NM_001172439.2 | P1 | |||
RPAP3-DT | ENST00000547799.5 | n.80-950A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.969 AC: 147510AN: 152184Hom.: 71525 Cov.: 32
GnomAD3 exomes AF: 0.964 AC: 232245AN: 240850Hom.: 112015 AF XY: 0.962 AC XY: 125397AN XY: 130348
GnomAD4 exome AF: 0.959 AC: 1384197AN: 1443366Hom.: 663891 Cov.: 26 AF XY: 0.958 AC XY: 688410AN XY: 718270
GnomAD4 genome AF: 0.969 AC: 147629AN: 152302Hom.: 71585 Cov.: 32 AF XY: 0.969 AC XY: 72178AN XY: 74476
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at