chr1-207113053-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000715.4(C4BPA):c.28G>A(p.Ala10Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,608,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A10V) has been classified as Uncertain significance.
Frequency
Consequence
NM_000715.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4BPA | NM_000715.4 | c.28G>A | p.Ala10Thr | missense_variant | 2/12 | ENST00000367070.8 | |
C4BPA | XM_005273251.3 | c.28G>A | p.Ala10Thr | missense_variant | 2/12 | ||
C4BPA | XM_005273252.5 | c.28G>A | p.Ala10Thr | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4BPA | ENST00000367070.8 | c.28G>A | p.Ala10Thr | missense_variant | 2/12 | 1 | NM_000715.4 | P1 | |
C4BPA | ENST00000421786.5 | c.28G>A | p.Ala10Thr | missense_variant | 2/5 | 4 | |||
C4BPA | ENST00000424088.1 | c.28G>A | p.Ala10Thr | missense_variant, NMD_transcript_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152114Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000217 AC: 53AN: 244464Hom.: 0 AF XY: 0.000212 AC XY: 28AN XY: 132350
GnomAD4 exome AF: 0.000113 AC: 164AN: 1455966Hom.: 0 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 724290
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152114Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10AN XY: 74312
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at