chr7-134318805-T-C

Variant summary

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

The XM_011516645.4(SLC35B4):c.77+1334A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 152,234 control chromosomes in the GnomAD database, including 1,896 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 0.099 (1896 hom., cov: 32)
• Consequence: SLC35B4 XM_011516645.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35B4	XM_011516645.4	c.77+1334A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0982 AC: 14941 AN: 152116 Hom.: 1890 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00597

Gnomad OTH AF: 0.0802

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

GnomAD4 genome AF: 0.0985 AC: 14997 AN: 152234 Hom.: 1896 Cov.: 32 AF XY: 0.0973 AC XY: 7244 AN XY: 74434

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.0385

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.00597

Gnomad4 OTH AF: 0.0794

Alfa AF: 0.0207 Hom.: 381

Bravo AF: 0.112

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1643031; hg19: chr7-134003557;