rs142105038
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022369.4(STRA6):c.173C>T(p.Ser58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,613,496 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_022369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRA6 | NM_022369.4 | c.173C>T | p.Ser58Leu | missense_variant | 3/19 | ENST00000395105.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRA6 | ENST00000395105.9 | c.173C>T | p.Ser58Leu | missense_variant | 3/19 | 1 | NM_022369.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00723 AC: 1101AN: 152194Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.00204 AC: 509AN: 249616Hom.: 7 AF XY: 0.00144 AC XY: 195AN XY: 135252
GnomAD4 exome AF: 0.000769 AC: 1123AN: 1461184Hom.: 18 Cov.: 32 AF XY: 0.000634 AC XY: 461AN XY: 726942
GnomAD4 genome ? AF: 0.00722 AC: 1099AN: 152312Hom.: 16 Cov.: 32 AF XY: 0.00693 AC XY: 516AN XY: 74464
ClinVar
Submissions by phenotype
Matthew-Wood syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 04, 2020 | This variant is associated with the following publications: (PMID: 30653986) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at