ENST00000547342.1:c.281-10027T>C

Variant names:

• chr12-113409737-A-G
• rs1559997
• ENST00000547342.1:c.281-10027T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547342.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDS	ENST00000547342.1	TSL:5	c.281-10027T>C		intron	N/A	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

African (AFR) AF: 0.0851 AC: 3515 AN: 41324

American (AMR) AF: 0.0409 AC: 624 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3470

East Asian (EAS) AF: 0.0861 AC: 446 AN: 5178

South Asian (SAS) AF: 0.0465 AC: 224 AN: 4822

European-Finnish (FIN) AF: 0.0145 AC: 154 AN: 10616

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0314 AC: 2135 AN: 68008

Other (OTH) AF: 0.0563 AC: 119 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0060
DANN	Benign	0.24
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1559997; hg19: chr12-113847542;