rs1463502

chr1-234135601-T-C

Variant summary

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

The NM_173508.4(SLC35F3):c.284-95816T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,096 control chromosomes in the GnomAD database, including 6,014 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 0.24 (6014 hom., cov: 32)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F3	NM_173508.4	c.284-95816T>C		intron_variant		ENST00000366618.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F3	ENST00000366618.8	c.284-95816T>C		intron_variant		2	NM_173508.4

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36647 AN: 151978 Hom.: 6000 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.241 AC: 36705 AN: 152096 Hom.: 6014 Cov.: 32 AF XY: 0.247 AC XY: 18350 AN XY: 74334

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.240

Alfa AF: 0.164 Hom.: 3101

Bravo AF: 0.264

Asia WGS AF: 0.476 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.9
Dann	Benign	0.68

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: rs1463502; hg19: chr1-234271347;