rs3799255

Positions:

• chr6-8428964-T-C

Variant summary

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

The NM_001370476.2(SLC35B3):​c.297+900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,936 control chromosomes in the GnomAD database, including 19,865 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 0.50 (19865 hom., cov: 32)
• Consequence: SLC35B3 NM_001370476.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

SLC35B3 (HGNC:21601): (solute carrier family 35 member B3) This gene is a member of the solute carrier family. The encoded protein is involved in the transport of 3-prime phosphoadenosine 5-prime phosphosulfate (PAPS) from the nucleus or the cytosol to the Golgi lumen. This gene has been reported to be expressed preferentially in the human colon tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35B3	NM_001370479.2	c.201+900A>G		intron_variant		ENST00000710437.1
SLC35B3	NR_109913.2	n.658+900A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35B3	ENST00000710437.1	c.201+900A>G		intron_variant			NM_001370479.2	P1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75808 AN: 151818 Hom.: 19830 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.500 AC: 75904 AN: 151936 Hom.: 19865 Cov.: 32 AF XY: 0.499 AC XY: 37011 AN XY: 74234

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.481

Alfa AF: 0.441 Hom.: 6706

Bravo AF: 0.511

Asia WGS AF: 0.511 AC: 1771 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.46

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: rs3799255; hg19: chr6-8429197;