rs11969985

chr6-1922673-G-A

Variant summary

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

The NM_001500.4(GMDS):c.771+7430C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,080 control chromosomes in the GnomAD database, including 2,621 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 0.18 (2621 hom., cov: 32)
• Consequence: GMDS NM_001500.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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]

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 (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GMDS	NM_001500.4	c.771+7430C>T		intron_variant		ENST00000380815.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GMDS	ENST00000380815.5	c.771+7430C>T		intron_variant		1	NM_001500.4	P1
GMDS	ENST00000530927.5	c.681+7430C>T		intron_variant		1
GMDS	ENST00000380805.6	n.897+7430C>T		intron_variant, non_coding_transcript_variant		2
GMDS	ENST00000531690.5	n.250+7430C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27434 AN: 151962 Hom.: 2609 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.181 AC: 27487 AN: 152080 Hom.: 2621 Cov.: 32 AF XY: 0.184 AC XY: 13665 AN XY: 74328

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.156

Alfa AF: 0.152 Hom.: 864

Bravo AF: 0.175

Asia WGS AF: 0.163 AC: 565 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	4.4
Dann	Benign	0.22

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: rs11969985; hg19: chr6-1922907;