rs1543468

Positions:

• chr1-234212679-T-C
• chr1-234212679-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.284-18738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,130 control chromosomes in the GnomAD database, including 13,274 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 0.40 (13274 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F3	NM_173508.4	c.284-18738T>C		intron_variant		ENST00000366618.8
LOC124904553	XR_007066948.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F3	ENST00000366618.8	c.284-18738T>C		intron_variant		2	NM_173508.4
	ENST00000412483.1	n.1650A>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60335 AN: 152010 Hom.: 13246 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.408

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.397 AC: 60412 AN: 152130 Hom.: 13274 Cov.: 33 AF XY: 0.404 AC XY: 30028 AN XY: 74370

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.413

Alfa AF: 0.355 Hom.: 1313

Bravo AF: 0.414

Asia WGS AF: 0.596 AC: 2067 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	2.8
DANN	Benign	0.65

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: rs1543468; hg19: chr1-234348425;