chr6-8428964-T-C

Variant names:

• chr6-8428964-T-C
• rs3799255
• NM_001370479.2:c.201+900A>G

Variant summary

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

The NM_001370479.2(SLC35B3):​c.201+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_001370479.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 publications found

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]

ENSG00000285216 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC35B3	NM_001370479.2	c.201+900A>G		intron_variant	Intron 2 of 9	ENST00000710437.1	NP_001357408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35B3	ENST00000710437.1	c.201+900A>G		intron_variant	Intron 2 of 9		NM_001370479.2	ENSP00000518269.1

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

African (AFR) AF: 0.673 AC: 27920 AN: 41462

American (AMR) AF: 0.499 AC: 7616 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1507 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2270 AN: 5160

South Asian (SAS) AF: 0.504 AC: 2427 AN: 4812

European-Finnish (FIN) AF: 0.453 AC: 4784 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27995 AN: 67902

Other (OTH) AF: 0.481 AC: 1014 AN: 2110

Alfa AF: 0.441 Hom.: 7581

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
PhyloP100		-1.3
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: rs3799255; hg19: chr6-8429197;