rs1619682

chr7-134311951-T-G

Variant summary

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

The NM_032826.5(SLC35B4):c.78-2472A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,008 control chromosomes in the GnomAD database, including 18,250 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 0.49 (18250 hom., cov: 32)
• Consequence: SLC35B4 NM_032826.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

SLC35B4 (HGNC:20584): (solute carrier family 35 member B4) Glycosyltransferases, such as SLC35B4, transport nucleotide sugars from the cytoplasm where they are synthesized, to the Golgi apparatus where they are utilized in the synthesis of glycoproteins, glycolipids, and proteoglycans (Ashikov et al., 2005 [PubMed 15911612]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35B4	NM_032826.5	c.78-2472A>C		intron_variant		ENST00000378509.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35B4	ENST00000378509.9	c.78-2472A>C		intron_variant		1	NM_032826.5	P1
SLC35B4	ENST00000470969.2	c.78-2472A>C		intron_variant		1
SLC35B4	ENST00000416907.5	c.78-2472A>C		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73695 AN: 151888 Hom.: 18206 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.485 AC: 73791 AN: 152008 Hom.: 18250 Cov.: 32 AF XY: 0.484 AC XY: 35929 AN XY: 74284

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.475

Alfa AF: 0.485 Hom.: 2254

Bravo AF: 0.496

Asia WGS AF: 0.411 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	6.7
Dann	Benign	0.26

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: rs1619682; hg19: chr7-133996703;