7-134318805-T-C

Variant names:

• chr7-134318805-T-C
• rs1643031
• XM_011516645.4:c.77+1334A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.287 AC: 11908 AN: 41498

American (AMR) AF: 0.0659 AC: 1009 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5180

South Asian (SAS) AF: 0.0385 AC: 186 AN: 4828

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00597 AC: 406 AN: 68022

Other (OTH) AF: 0.0794 AC: 168 AN: 2116

Alfa AF: 0.0365 Hom.: 2127

Bravo AF: 0.112

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1643031; hg19: chr7-134003557;