rs2045520

chr1-234168223-G-T

Variant summary

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

The NM_173508.4(SLC35F3):c.284-63194G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,212 control chromosomes in the GnomAD database, including 39,479 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 0.65 (39479 hom., cov: 33)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.919

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F3	NM_173508.4	c.284-63194G>T		intron_variant		ENST00000366618.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F3	ENST00000366618.8	c.284-63194G>T		intron_variant		2	NM_173508.4

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98633 AN: 152094 Hom.: 39478 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.648 AC: 98633 AN: 152212 Hom.: 39479 Cov.: 33 AF XY: 0.641 AC XY: 47702 AN XY: 74412

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.675

Alfa AF: 0.772 Hom.: 6174

Bravo AF: 0.605

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.6
Dann	Benign	0.83

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: rs2045520; hg19: chr1-234303969;