rs2045520

Variant names:

• chr1-234168223-G-T
• rs2045520
• NM_173508.4:c.284-63194G>T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	NM_173508.4	MANE Select	c.284-63194G>T		intron	N/A	NP_775779.1	Q8IY50-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	ENST00000366618.8	TSL:2 MANE Select	c.284-63194G>T		intron	N/A	ENSP00000355577.3	Q8IY50-2

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

African (AFR) AF: 0.215 AC: 8936 AN: 41524

American (AMR) AF: 0.601 AC: 9186 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3073 AN: 3468

East Asian (EAS) AF: 0.142 AC: 733 AN: 5168

South Asian (SAS) AF: 0.652 AC: 3140 AN: 4816

European-Finnish (FIN) AF: 0.868 AC: 9208 AN: 10606

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61840 AN: 68020

Other (OTH) AF: 0.675 AC: 1425 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.83
PhyloP100		0.92
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: rs2045520; hg19: chr1-234303969;