chr1-207113035-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000715.4(C4BPA):c.10C>G(p.Pro4Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00399 in 1,597,298 control chromosomes in the GnomAD database, including 222 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P4Q) has been classified as Benign.
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.10C>G | p.Pro4Ala | missense_variant | 2/12 | ENST00000367070.8 | |
C4BPA | XM_005273251.3 | c.10C>G | p.Pro4Ala | missense_variant | 2/12 | ||
C4BPA | XM_005273252.5 | c.10C>G | p.Pro4Ala | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4BPA | ENST00000367070.8 | c.10C>G | p.Pro4Ala | missense_variant | 2/12 | 1 | NM_000715.4 | P1 | |
C4BPA | ENST00000421786.5 | c.10C>G | p.Pro4Ala | missense_variant | 2/5 | 4 | |||
C4BPA | ENST00000424088.1 | c.10C>G | p.Pro4Ala | missense_variant, NMD_transcript_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0216 AC: 3280AN: 152100Hom.: 120 Cov.: 31
GnomAD3 exomes AF: 0.00584 AC: 1368AN: 234326Hom.: 54 AF XY: 0.00421 AC XY: 536AN XY: 127270
GnomAD4 exome AF: 0.00214 AC: 3090AN: 1445080Hom.: 102 Cov.: 31 AF XY: 0.00180 AC XY: 1291AN XY: 718912
GnomAD4 genome ? AF: 0.0216 AC: 3281AN: 152218Hom.: 120 Cov.: 31 AF XY: 0.0206 AC XY: 1536AN XY: 74432
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