7-134312808-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
SLC35B4NM_032826.5 linkuse as main transcriptc.78-3329G>A intron_variant ENST00000378509.9 NP_116215.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC35B4ENST00000378509.9 linkuse as main transcriptc.78-3329G>A intron_variant 1 NM_032826.5 ENSP00000367770 P1Q969S0-1
SLC35B4ENST00000470969.2 linkuse as main transcriptc.78-3329G>A intron_variant 1 ENSP00000485857 Q969S0-2
SLC35B4ENST00000416907.5 linkuse as main transcriptc.78-3329G>A intron_variant, NMD_transcript_variant 1 ENSP00000405445

Frequencies

GnomAD3 genomes
AF:
0.339
AC:
51505
AN:
151828
Hom.:
10743
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.456
Gnomad4 ASJ
AF:
0.301
Gnomad4 EAS
AF:
0.132
Gnomad4 SAS
AF:
0.494
Gnomad4 FIN
AF:
0.358
Gnomad4 NFE
AF:
0.458
Gnomad4 OTH
AF:
0.345
Alfa
AF:
0.430
Hom.:
6562
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10488428; hg19: chr7-133997560; API