rs3215922

Variant names:

• chr9-6532510-TAAA-T
• rs3215922
• NM_000170.3:c.*504_*506delTTT

Your query was ambiguous. Multiple possible variants found:

• chr9-6532510-TAAA-T
• chr9-6532510-TAAA-TA
• chr9-6532510-TAAA-TAA
• chr9-6532510-TAAA-TAAAA
• chr9-6532510-TAAA-TAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000170.3(GLDC):​c.*504_*506delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 143,818 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000097 (0 hom., cov: 22)
  • Exomes 𝑓: 0.0021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GLDC NM_000170.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

Genes affected

GLDC (HGNC:4313): (glycine decarboxylase) Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide dehydrogenase). The protein encoded by this gene is the P protein, which binds to glycine and enables the methylamine group from glycine to be transferred to the T protein. Defects in this gene are a cause of nonketotic hyperglycinemia (NKH).[provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLDC	NM_000170.3	c.*504_*506delTTT		3_prime_UTR_variant	Exon 25 of 25	ENST00000321612.8	NP_000161.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLDC	ENST00000321612	c.*504_*506delTTT		3_prime_UTR_variant	Exon 25 of 25	1	NM_000170.3	ENSP00000370737.4

Frequencies

GnomAD3 genomes AF: 0.0000973 AC: 14 AN: 143818 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000138

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000221

Gnomad FIN AF: 0.000228

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000122

Gnomad OTH AF: 0.000514

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00212 AC: 9 AN: 4244 Hom.: 0 AF XY: 0.00270 AC XY: 6 AN XY: 2226

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00120

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0185

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00255

Gnomad4 NFE exome AF: 0.00254

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000973 AC: 14 AN: 143818 Hom.: 0 Cov.: 22 AF XY: 0.000143 AC XY: 10 AN XY: 69796

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000138

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000221

Gnomad4 FIN AF: 0.000228

Gnomad4 NFE AF: 0.000122

Gnomad4 OTH AF: 0.000514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs3215922; hg19: chr9-6532510;