6-87477214-A-G

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.17-148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 656,482 control chromosomes in the GnomAD database, including 44,335 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.38 (10847 hom., cov: 31)
  • Exomes 𝑓: 0.36 (33488 hom.)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.574

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=-0.82).
• BP6: Variant 6-87477214-A-G is Benign according to our data. Variant chr6-87477214-A-G is described in ClinVar as [Benign]. Clinvar id is 1276097.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35A1	NM_006416.5	c.17-148A>G		intron_variant		ENST00000369552.9
SLC35A1	NM_001168398.2	c.17-148A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A1	ENST00000369552.9	c.17-148A>G		intron_variant		1	NM_006416.5	P1
SLC35A1	ENST00000369556.7	c.17-148A>G		intron_variant		1
SLC35A1	ENST00000369557.9	c.17-148A>G		intron_variant		2
SLC35A1	ENST00000464978.5	n.92-148A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57191 AN: 151374 Hom.: 10835 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.377

GnomAD4 exome AF: 0.355 AC: 179482 AN: 504988 Hom.: 33488 AF XY: 0.356 AC XY: 95589 AN XY: 268230

Gnomad4 AFR exome AF: 0.402

Gnomad4 AMR exome AF: 0.508

Gnomad4 ASJ exome AF: 0.351

Gnomad4 EAS exome AF: 0.303

Gnomad4 SAS exome AF: 0.375

Gnomad4 FIN exome AF: 0.321

Gnomad4 NFE exome AF: 0.346

Gnomad4 OTH exome AF: 0.358

GnomAD4 genome AF: 0.378 AC: 57221 AN: 151494 Hom.: 10847 Cov.: 31 AF XY: 0.376 AC XY: 27858 AN XY: 74010

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.372

Alfa AF: 0.373 Hom.: 1257

Bravo AF: 0.389

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

Jun 29, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.2
Dann	Benign	0.67

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: rs16879893; hg19: chr6-88186932; COSMIC: COSV65780610; COSMIC: COSV65780610;