rs1458597

Variant names:

• chr1-234019116-T-C
• rs1458597
• NM_173508.4:c.283+113358T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173508.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	NM_173508.4	MANE Select	c.283+113358T>C		intron	N/A	NP_775779.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	ENST00000366618.8	TSL:2 MANE Select	c.283+113358T>C		intron	N/A	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

African (AFR) AF: 0.215 AC: 8903 AN: 41480

American (AMR) AF: 0.0529 AC: 809 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3470

East Asian (EAS) AF: 0.155 AC: 798 AN: 5160

South Asian (SAS) AF: 0.0838 AC: 404 AN: 4822

European-Finnish (FIN) AF: 0.0560 AC: 594 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00849 AC: 577 AN: 67986

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0295 Hom.: 1157

Bravo AF: 0.0844

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.060
DANN	Benign	0.60
PhyloP100		-1.8
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: rs1458597; hg19: chr1-234154862;