2-233309224-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000541.5(SAG):c.35C>T(p.Pro12Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000535 in 1,613,684 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P12P) has been classified as Likely benign.
Frequency
Consequence
NM_000541.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAG | NM_000541.5 | c.35C>T | p.Pro12Leu | missense_variant | 2/16 | ENST00000409110.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAG | ENST00000409110.6 | c.35C>T | p.Pro12Leu | missense_variant | 2/16 | 5 | NM_000541.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000582 AC: 145AN: 249040Hom.: 1 AF XY: 0.000592 AC XY: 80AN XY: 135110
GnomAD4 exome AF: 0.000556 AC: 812AN: 1461500Hom.: 3 Cov.: 30 AF XY: 0.000554 AC XY: 403AN XY: 727034
GnomAD4 genome AF: 0.000342 AC: 52AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at