rs13010956
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145259.3(ACVR1C):c.544+63A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 1,522,714 control chromosomes in the GnomAD database, including 141,801 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.39 ( 11831 hom., cov: 31)
Exomes 𝑓: 0.43 ( 129970 hom. )
Consequence
ACVR1C
NM_145259.3 intron
NM_145259.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.222
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 2-157556030-T-C is Benign according to our data. Variant chr2-157556030-T-C is described in ClinVar as [Benign]. Clinvar id is 1225542.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACVR1C | NM_145259.3 | c.544+63A>G | intron_variant | ENST00000243349.13 | |||
ACVR1C | NM_001111031.2 | c.394+63A>G | intron_variant | ||||
ACVR1C | NM_001111032.2 | c.305-5638A>G | intron_variant | ||||
ACVR1C | NM_001111033.2 | c.305-11418A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACVR1C | ENST00000243349.13 | c.544+63A>G | intron_variant | 1 | NM_145259.3 | P1 | |||
ACVR1C | ENST00000335450.7 | c.305-5638A>G | intron_variant | 1 | |||||
ACVR1C | ENST00000348328.9 | c.305-11418A>G | intron_variant | 1 | |||||
ACVR1C | ENST00000409680.7 | c.394+63A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.387 AC: 58815AN: 151848Hom.: 11817 Cov.: 31
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GnomAD4 exome AF: 0.430 AC: 589931AN: 1370748Hom.: 129970 AF XY: 0.427 AC XY: 288854AN XY: 676872
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GnomAD4 genome ? AF: 0.387 AC: 58854AN: 151966Hom.: 11831 Cov.: 31 AF XY: 0.380 AC XY: 28207AN XY: 74252
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at