2-119461998-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_002980.3(SCTR):c.639G>A(p.Ala213=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000205 in 1,598,800 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002980.3 splice_region, synonymous
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 |
---|---|---|---|---|---|---|---|
SCTR | NM_002980.3 | c.639G>A | p.Ala213= | splice_region_variant, synonymous_variant | 7/13 | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.639G>A | p.Ala213= | splice_region_variant, synonymous_variant | 7/13 | 1 | NM_002980.3 | P1 | |
SCTR | ENST00000627145.1 | c.714G>A | p.Ala238= | splice_region_variant, synonymous_variant | 8/8 | 5 | |||
SCTR | ENST00000630739.2 | c.435G>A | p.Ala145= | splice_region_variant, synonymous_variant | 8/8 | 5 | |||
SCTR | ENST00000485440.1 | n.1319G>A | splice_region_variant, non_coding_transcript_exon_variant | 4/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000642 AC: 154AN: 239748Hom.: 2 AF XY: 0.000571 AC XY: 74AN XY: 129608
GnomAD4 exome AF: 0.000196 AC: 283AN: 1446524Hom.: 5 Cov.: 31 AF XY: 0.000188 AC XY: 135AN XY: 718946
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 11, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at