rs9450716

chr6-87493123-G-A

Variant summary

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

The NM_006416.5(SLC35A1):c.195-7385G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,736 control chromosomes in the GnomAD database, including 12,208 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 0.40 (12208 hom., cov: 30)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35A1	NM_006416.5	c.195-7385G>A		intron_variant		ENST00000369552.9
SLC35A1	NM_001168398.2	c.195-7385G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A1	ENST00000369552.9	c.195-7385G>A		intron_variant		1	NM_006416.5	P1
SLC35A1	ENST00000369556.7	c.195-7385G>A		intron_variant		1
SLC35A1	ENST00000369557.9	c.195-7385G>A		intron_variant		2
SLC35A1	ENST00000464978.5	n.270-7385G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60305 AN: 151618 Hom.: 12195 Cov.: 30

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.398 AC: 60344 AN: 151736 Hom.: 12208 Cov.: 30 AF XY: 0.396 AC XY: 29335 AN XY: 74146

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.388

Alfa AF: 0.363 Hom.: 18900

Bravo AF: 0.412

Asia WGS AF: 0.347 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.34
Dann	Benign	0.51

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: rs9450716; hg19: chr6-88202841;