2-119452057-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002980.3(SCTR):c.874G>A(p.Ala292Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00405 in 1,608,034 control chromosomes in the GnomAD database, including 34 homozygotes. 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 (★).
Frequency
Consequence
NM_002980.3 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 |
---|---|---|---|---|---|---|---|
SCTR | NM_002980.3 | c.874G>A | p.Ala292Thr | missense_variant | 9/13 | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.874G>A | p.Ala292Thr | missense_variant | 9/13 | 1 | NM_002980.3 | P1 | |
SCTR | ENST00000485440.1 | n.1554G>A | non_coding_transcript_exon_variant | 6/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00378 AC: 575AN: 152198Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00375 AC: 916AN: 243946Hom.: 3 AF XY: 0.00396 AC XY: 520AN XY: 131316
GnomAD4 exome AF: 0.00408 AC: 5933AN: 1455720Hom.: 30 Cov.: 28 AF XY: 0.00412 AC XY: 2985AN XY: 723914
GnomAD4 genome ? AF: 0.00378 AC: 575AN: 152314Hom.: 4 Cov.: 33 AF XY: 0.00334 AC XY: 249AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 25, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at