rs1458597

Positions:

• chr1-234019116-T-C
• chr1-234019116-T-G

Variant summary

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

The NM_173508.4(SLC35F3):​c.283+113358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,140 control chromosomes in the GnomAD database, including 1,106 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 0.081 (1106 hom., cov: 32)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

SLC35F3 (HGNC:23616): (solute carrier family 35 member F3) Involved in thiamine transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35F3	NM_173508.4	c.283+113358T>C		intron_variant		ENST00000366618.8	NP_775779.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35F3	ENST00000366618.8	c.283+113358T>C		intron_variant		2	NM_173508.4	ENSP00000355577.3

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12294 AN: 152022 Hom.: 1098 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00849

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0811 AC: 12341 AN: 152140 Hom.: 1106 Cov.: 32 AF XY: 0.0843 AC XY: 6269 AN XY: 74400

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0529

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0838

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.00849

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0179 Hom.: 215

Bravo AF: 0.0844

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.060
DANN	Benign	0.60

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: rs1458597; hg19: chr1-234154862;