12-113409737-A-G

Position:

• chr12-113409737-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000547342.1(SDS):​c.281-10027T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,008 control chromosomes in the GnomAD database, including 262 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.050 (262 hom., cov: 31)
• Consequence: SDS ENST00000547342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113409737A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDS	ENST00000547342.1	c.281-10027T>C		intron_variant		5		ENSP00000449061.1

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7516 AN: 151892 Hom.: 252 Cov.: 31

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0540

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0497 AC: 7553 AN: 152008 Hom.: 262 Cov.: 31 AF XY: 0.0491 AC XY: 3651 AN XY: 74330

Gnomad4 AFR AF: 0.0851

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.0465

Gnomad4 FIN AF: 0.0145

Gnomad4 NFE AF: 0.0314

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0462 Hom.: 190

Bravo AF: 0.0532

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0060
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1559997; hg19: chr12-113847542;