chr1-111312237-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_201653.4(CHIA):c.103C>T(p.Arg35Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00234 in 1,614,084 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts 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. R35Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_201653.4 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 |
---|---|---|---|---|---|---|---|
CHIA | NM_201653.4 | c.103C>T | p.Arg35Trp | missense_variant | 4/12 | ENST00000369740.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHIA | ENST00000369740.6 | c.103C>T | p.Arg35Trp | missense_variant | 4/12 | 1 | NM_201653.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0124 AC: 1893AN: 152136Hom.: 33 Cov.: 31
GnomAD3 exomes AF: 0.00307 AC: 765AN: 249344Hom.: 15 AF XY: 0.00212 AC XY: 287AN XY: 135274
GnomAD4 exome AF: 0.00128 AC: 1878AN: 1461830Hom.: 36 Cov.: 33 AF XY: 0.00110 AC XY: 801AN XY: 727226
GnomAD4 genome ? AF: 0.0125 AC: 1901AN: 152254Hom.: 33 Cov.: 31 AF XY: 0.0116 AC XY: 861AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at