2-157543002-G-C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145259.3(ACVR1C):c.944-140C>G 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: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ACVR1C
NM_145259.3 intron
NM_145259.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0670
Genes affected
ACVR1C (HGNC:18123): (activin A receptor type 1C) ACVR1C is a type I receptor for the TGFB (see MIM 190180) family of signaling molecules. Upon ligand binding, type I receptors phosphorylate cytoplasmic SMAD transcription factors, which then translocate to the nucleus and interact directly with DNA or in complex with other transcription factors (Bondestam et al., 2001 [PubMed 12063393]).[supplied by OMIM, Mar 2008]
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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=-0.71).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACVR1C | NM_145259.3 | c.944-140C>G | intron_variant | Intron 5 of 8 | ENST00000243349.13 | NP_660302.2 | ||
ACVR1C | NM_001111031.2 | c.794-140C>G | intron_variant | Intron 5 of 8 | NP_001104501.1 | |||
ACVR1C | NM_001111032.2 | c.704-140C>G | intron_variant | Intron 4 of 7 | NP_001104502.1 | |||
ACVR1C | NM_001111033.2 | c.473-140C>G | intron_variant | Intron 3 of 6 | NP_001104503.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACVR1C | ENST00000243349.13 | c.944-140C>G | intron_variant | Intron 5 of 8 | 1 | NM_145259.3 | ENSP00000243349.7 | |||
ACVR1C | ENST00000409680.7 | c.794-140C>G | intron_variant | Intron 5 of 8 | 1 | ENSP00000387168.3 | ||||
ACVR1C | ENST00000335450.7 | c.704-140C>G | intron_variant | Intron 4 of 7 | 1 | ENSP00000335178.7 | ||||
ACVR1C | ENST00000348328.9 | c.473-140C>G | intron_variant | Intron 3 of 6 | 1 | ENSP00000335139.6 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 631460Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 327346
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
631460
Hom.:
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AC XY:
0
AN XY:
327346
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at