6-87477213-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_006416.5(SLC35A1):c.17-149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 647,730 control chromosomes in the GnomAD database, including 798 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.055 (263 hom., cov: 32)
  • Exomes 𝑓: 0.040 (535 hom.)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.576

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 6-87477213-C-T is Benign according to our data. Variant chr6-87477213-C-T is described in ClinVar as [Benign]. Clinvar id is 1248926.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35A1	NM_006416.5	c.17-149C>T		intron_variant		ENST00000369552.9
SLC35A1	NM_001168398.2	c.17-149C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A1	ENST00000369552.9	c.17-149C>T		intron_variant		1	NM_006416.5	P1
SLC35A1	ENST00000369556.7	c.17-149C>T		intron_variant		1
SLC35A1	ENST00000369557.9	c.17-149C>T		intron_variant		2
SLC35A1	ENST00000464978.5	n.92-149C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 8307 AN: 151200 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.0558

GnomAD4 exome AF: 0.0398 AC: 19769 AN: 496412 Hom.: 535 AF XY: 0.0394 AC XY: 10400 AN XY: 263874

Gnomad4 AFR exome AF: 0.0862

Gnomad4 AMR exome AF: 0.0240

Gnomad4 ASJ exome AF: 0.0202

Gnomad4 EAS exome AF: 0.000170

Gnomad4 SAS exome AF: 0.0256

Gnomad4 FIN exome AF: 0.0621

Gnomad4 NFE exome AF: 0.0442

Gnomad4 OTH exome AF: 0.0412

GnomAD4 genome AF: 0.0549 AC: 8309 AN: 151318 Hom.: 263 Cov.: 32 AF XY: 0.0546 AC XY: 4034 AN XY: 73934

Gnomad4 AFR AF: 0.0864

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.0202

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0488

Gnomad4 OTH AF: 0.0548

Alfa AF: 0.0610 Hom.: 34

Bravo AF: 0.0534

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 09, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.25
Dann	Benign	0.41

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: rs78238771; hg19: chr6-88186931;