7-134312808-C-T

Variant names:

• chr7-134312808-C-T
• rs10488428
• NM_032826.5:c.78-3329G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032826.5(SLC35B4):​c.78-3329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,946 control chromosomes in the GnomAD database, including 10,753 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 0.34 (10753 hom., cov: 32)
• Consequence: SLC35B4 NM_032826.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35B4	NM_032826.5	c.78-3329G>A		intron_variant	Intron 1 of 9	ENST00000378509.9	NP_116215.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35B4	ENST00000378509.9	c.78-3329G>A		intron_variant	Intron 1 of 9	1	NM_032826.5	ENSP00000367770.4
SLC35B4	ENST00000470969.2	c.78-3329G>A		intron_variant	Intron 1 of 7	1		ENSP00000485857.1
SLC35B4	ENST00000416907.5	n.78-3329G>A		intron_variant	Intron 1 of 8	1		ENSP00000405445.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51505 AN: 151828 Hom.: 10743 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.339 AC: 51515 AN: 151946 Hom.: 10753 Cov.: 32 AF XY: 0.340 AC XY: 25242 AN XY: 74260

African (AFR) AF: 0.102 AC: 4242 AN: 41450

American (AMR) AF: 0.456 AC: 6958 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3468

East Asian (EAS) AF: 0.132 AC: 682 AN: 5168

South Asian (SAS) AF: 0.494 AC: 2377 AN: 4814

European-Finnish (FIN) AF: 0.358 AC: 3773 AN: 10542

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31127 AN: 67924

Other (OTH) AF: 0.345 AC: 727 AN: 2108

Alfa AF: 0.427 Hom.: 7285

Bravo AF: 0.331

Asia WGS AF: 0.291 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10488428; hg19: chr7-133997560;