chr12-7062500-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001734.5(C1S):c.31G>T(p.Ala11Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000775 in 1,613,290 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. A11V) has been classified as Likely benign.
Frequency
Consequence
NM_001734.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1S | NM_001734.5 | c.31G>T | p.Ala11Ser | missense_variant | 3/12 | ENST00000360817.10 | |
C1S | NM_201442.4 | c.31G>T | p.Ala11Ser | missense_variant | 3/12 | ||
C1S | NM_001346850.2 | c.-288-390G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1S | ENST00000360817.10 | c.31G>T | p.Ala11Ser | missense_variant | 3/12 | 1 | NM_001734.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251290Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135810
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461100Hom.: 0 Cov.: 32 AF XY: 0.0000482 AC XY: 35AN XY: 726868
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at