GeneBe

rs1818702

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001386867.1(C12orf42):​c.*22-48240G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)

Consequence

C12orf42
NM_001386867.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00800
Variant links:
Genes affected
C12orf42 (HGNC:24729): (chromosome 12 open reading frame 42)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C12orf42NM_001386867.1 linkc.*22-48240G>T intron_variant Intron 6 of 6 NP_001373796.1
C12orf42NR_170336.1 linkn.1120-48240G>T intron_variant Intron 10 of 10
C12orf42XR_001748690.2 linkn.668+48352G>T intron_variant Intron 10 of 11

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000257703ENST00000548415.2 linkn.339-48240G>T intron_variant Intron 2 of 2 4
ENSG00000257703ENST00000548594.6 linkn.168-48240G>T intron_variant Intron 2 of 2 5
ENSG00000257703ENST00000660834.1 linkn.192-48240G>T intron_variant Intron 2 of 2
ENSG00000257703ENST00000667540.1 linkn.262-6337G>T intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.8
DANN
Benign
0.46

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: rs1818702; hg19: chr12-103523555; API