11-45804395-G-A

Variant summary

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

The ENST00000442528.2(SLC35C1):c.-154G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 767,722 control chromosomes in the GnomAD database, including 2,378 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.086 (721 hom., cov: 34)
  • Exomes 𝑓: 0.069 (1657 hom.)
• Consequence: SLC35C1 ENST00000442528.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.79

Genes affected

SLC35C1 (HGNC:20197): (solute carrier family 35 member C1) This gene encodes a GDP-fucose transporter that is found in the Golgi apparatus. Mutations in this gene result in congenital disorder of glycosylation type IIc. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 11-45804395-G-A is Benign according to our data. Variant chr11-45804395-G-A is described in ClinVar as [Benign]. Clinvar id is 1283904.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35C1	NM_001145266.1	c.-57G>A		5_prime_UTR_variant	1/3
SLC35C1	NM_001145265.2			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35C1	ENST00000442528.2	c.-154G>A		5_prime_UTR_variant	1/3	1		A1
SLC35C1	ENST00000526817.2	c.-57G>A		5_prime_UTR_variant	1/3	2		A1

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13110 AN: 152196 Hom.: 720 Cov.: 34

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0817

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.0764

GnomAD4 exome AF: 0.0693 AC: 42634 AN: 615412 Hom.: 1657 Cov.: 8 AF XY: 0.0694 AC XY: 19903 AN XY: 286954

Gnomad4 AFR exome AF: 0.154

Gnomad4 AMR exome AF: 0.0290

Gnomad4 ASJ exome AF: 0.0177

Gnomad4 EAS exome AF: 0.00114

Gnomad4 SAS exome AF: 0.0509

Gnomad4 FIN exome AF: 0.0891

Gnomad4 NFE exome AF: 0.0688

Gnomad4 OTH exome AF: 0.0659

GnomAD4 genome AF: 0.0861 AC: 13112 AN: 152310 Hom.: 721 Cov.: 34 AF XY: 0.0849 AC XY: 6321 AN XY: 74476

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0455

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.0756

Alfa AF: 0.0892 Hom.: 87

Bravo AF: 0.0828

Asia WGS AF: 0.0240 AC: 84 AN: 3478

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 23, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	4.2
Dann	Benign	0.94

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs76951039; hg19: chr11-45825946;