Genetic Variant GMDS:c.643+10505_643+10508dupTATA (chr6-1949358-G-GTATA) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001500.4(GMDS):c.643+10505_643+10508dupTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 26)

Consequence

GMDS
NM_001500.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

GMDS (HGNC:4369): (GDP-mannose 4,6-dehydratase) GDP-mannose 4,6-dehydratase (GMD; EC 4.2.1.47) catalyzes the conversion of GDP-mannose to GDP-4-keto-6-deoxymannose, the first step in the synthesis of GDP-fucose from GDP-mannose, using NADP+ as a cofactor. The second and third steps of the pathway are catalyzed by a single enzyme, GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase, designated FX in humans (MIM 137020).[supplied by OMIM, Aug 2009]

GMDS links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GMDS	NM_001500.4 link	c.643+10505_643+10508dupTATA		intron_variant	Intron 6 of 10	ENST00000380815.5	NP_001491.1	O60547-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GMDS	ENST00000380815.5 link	c.643+10508_643+10509insTATA	intron_variant	Intron 6 of 10	1	NM_001500.4	ENSP00000370194.4	O60547-1
GMDS	ENST00000530927.5 link	c.553+10508_553+10509insTATA	intron_variant	Intron 6 of 10	1		ENSP00000436726.1	O60547-2
GMDS	ENST00000530459.1 link	n.396+10508_396+10509insTATA	intron_variant	Intron 3 of 3	3
GMDS	ENST00000531690.5 link	n.122+10508_122+10509insTATA	intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

No publications associated with this variant yet.