12-113398839-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006843.3(SDS):c.201C>T(p.Asn67=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00176 in 1,604,520 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 2 hom. )
Consequence
SDS
NM_006843.3 synonymous
NM_006843.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.959
Genes affected
SDS (HGNC:10691): (serine dehydratase) This gene encodes one of three enzymes that are involved in metabolizing serine and glycine. L-serine dehydratase converts L-serine to pyruvate and ammonia and requires pyridoxal phosphate as a cofactor. The encoded protein can also metabolize threonine to NH4+ and 2-ketobutyrate. The encoded protein is found predominantly in the liver. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 12-113398839-G-A is Benign according to our data. Variant chr12-113398839-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 726251.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=-0.959 with no splicing effect.
BS2
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High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| SDS | NM_006843.3 | c.201C>T | p.Asn67= | synonymous_variant | 4/8 | ENST00000257549.9 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SDS | ENST00000257549.9 | c.201C>T | p.Asn67= | synonymous_variant | 4/8 | 2 | NM_006843.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00124 AC: 189AN: 152228Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000861 AC: 196AN: 227592Hom.: 0 AF XY: 0.000946 AC XY: 117AN XY: 123634
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GnomAD4 exome AF: 0.00182 AC: 2639AN: 1452174Hom.: 2 Cov.: 32 AF XY: 0.00175 AC XY: 1260AN XY: 721772
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GnomAD4 genome ? AF: 0.00124 AC: 189AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.00113 AC XY: 84AN XY: 74504
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 27, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at