12-113397314-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_006843.3(SDS):​c.504C>T​(p.Gly168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000034 ( 0 hom. )

Consequence

SDS
NM_006843.3 synonymous

Scores

3
12

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.64
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.058894426).
BP6
Variant 12-113397314-G-A is Benign according to our data. Variant chr12-113397314-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 745995.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.64 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SDSNM_006843.3 linkuse as main transcriptc.504C>T p.Gly168= synonymous_variant 6/8 ENST00000257549.9 NP_006834.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SDSENST00000257549.9 linkuse as main transcriptc.504C>T p.Gly168= synonymous_variant 6/82 NM_006843.3 ENSP00000257549 P1
SDSENST00000552280.5 linkuse as main transcriptc.232C>T p.Arg78Trp missense_variant 3/33 ENSP00000449833
SDSENST00000553112.5 linkuse as main transcriptn.625C>T non_coding_transcript_exon_variant 6/62

Frequencies

GnomAD3 genomes
AF:
0.000204
AC:
31
AN:
152188
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000676
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000598
AC:
15
AN:
250840
Hom.:
0
AF XY:
0.0000442
AC XY:
6
AN XY:
135640
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.000173
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000353
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000342
AC:
50
AN:
1461738
Hom.:
0
Cov.:
31
AF XY:
0.0000275
AC XY:
20
AN XY:
727164
show subpopulations
Gnomad4 AFR exome
AF:
0.000777
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000126
Gnomad4 OTH exome
AF:
0.0000828
GnomAD4 genome
AF:
0.000197
AC:
30
AN:
152306
Hom.:
0
Cov.:
32
AF XY:
0.000201
AC XY:
15
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.000674
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000161
Hom.:
0
Bravo
AF:
0.000249
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000494
AC:
6
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.62
T
BayesDel_noAF
Benign
-0.76
CADD
Benign
5.6
DANN
Uncertain
1.0
DEOGEN2
Benign
0.025
T
Eigen
Benign
-0.83
Eigen_PC
Benign
-0.99
FATHMM_MKL
Benign
0.025
N
LIST_S2
Benign
0.45
T
MetaRNN
Benign
0.059
T
MetaSVM
Benign
-0.87
T
MutationTaster
Benign
1.0
D
PROVEAN
Benign
-2.3
N
REVEL
Benign
0.10
Sift
Uncertain
0.0070
D
Sift4G
Uncertain
0.012
D
MVP
0.15
ClinPred
0.27
T
GERP RS
-3.9

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs185843116; hg19: chr12-113835119; COSMIC: COSV57452566; COSMIC: COSV57452566; API