GeneBe

rs3046543

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001500.4(GMDS):​c.643+10505_643+10508del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,874 control chromosomes in the GnomAD database, including 5,931 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5931 hom., cov: 25)

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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GMDSNM_001500.4 linkuse as main transcriptc.643+10505_643+10508del intron_variant ENST00000380815.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GMDSENST00000380815.5 linkuse as main transcriptc.643+10505_643+10508del intron_variant 1 NM_001500.4 P1O60547-1
GMDSENST00000530927.5 linkuse as main transcriptc.553+10505_553+10508del intron_variant 1 O60547-2
GMDSENST00000530459.1 linkuse as main transcriptn.396+10505_396+10508del intron_variant, non_coding_transcript_variant 3
GMDSENST00000531690.5 linkuse as main transcriptn.122+10505_122+10508del intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37153
AN:
151756
Hom.:
5894
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.458
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.214
Gnomad ASJ
AF:
0.120
Gnomad EAS
AF:
0.200
Gnomad SAS
AF:
0.132
Gnomad FIN
AF:
0.217
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.148
Gnomad OTH
AF:
0.206
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37242
AN:
151874
Hom.:
5931
Cov.:
25
AF XY:
0.247
AC XY:
18325
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.459
Gnomad4 AMR
AF:
0.214
Gnomad4 ASJ
AF:
0.120
Gnomad4 EAS
AF:
0.200
Gnomad4 SAS
AF:
0.131
Gnomad4 FIN
AF:
0.217
Gnomad4 NFE
AF:
0.148
Gnomad4 OTH
AF:
0.206
Alfa
AF:
0.211
Hom.:
512
Bravo
AF:
0.250
Asia WGS
AF:
0.178
AC:
618
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

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

Other links and lift over

dbSNP: rs3046543; hg19: chr6-1949592; API