chr1-207114136-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000715.4(C4BPA):c.179C>T(p.Ala60Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 1,613,178 control chromosomes in the GnomAD database, including 352 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000715.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4BPA | NM_000715.4 | c.179C>T | p.Ala60Val | missense_variant | 3/12 | ENST00000367070.8 | |
C4BPA | XM_005273251.3 | c.179C>T | p.Ala60Val | missense_variant | 3/12 | ||
C4BPA | XM_005273252.5 | c.179C>T | p.Ala60Val | missense_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4BPA | ENST00000367070.8 | c.179C>T | p.Ala60Val | missense_variant | 3/12 | 1 | NM_000715.4 | P1 | |
C4BPA | ENST00000421786.5 | c.179C>T | p.Ala60Val | missense_variant | 3/5 | 4 | |||
C4BPA | ENST00000424088.1 | c.179C>T | p.Ala60Val | missense_variant, NMD_transcript_variant | 3/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0263 AC: 3995AN: 152006Hom.: 159 Cov.: 31
GnomAD3 exomes AF: 0.00679 AC: 1703AN: 250926Hom.: 81 AF XY: 0.00486 AC XY: 659AN XY: 135676
GnomAD4 exome AF: 0.00277 AC: 4045AN: 1461054Hom.: 193 Cov.: 30 AF XY: 0.00238 AC XY: 1729AN XY: 726878
GnomAD4 genome AF: 0.0263 AC: 3999AN: 152124Hom.: 159 Cov.: 31 AF XY: 0.0254 AC XY: 1890AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at