rs10797531

chr1-234140268-C-T

Variant summary

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

The NM_173508.4(SLC35F3):c.284-91149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,878 control chromosomes in the GnomAD database, including 15,486 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 0.42 (15486 hom., cov: 31)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

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 = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F3	NM_173508.4	c.284-91149C>T		intron_variant		ENST00000366618.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F3	ENST00000366618.8	c.284-91149C>T		intron_variant		2	NM_173508.4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64074 AN: 151760 Hom.: 15490 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.0246

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.422 AC: 64090 AN: 151878 Hom.: 15486 Cov.: 31 AF XY: 0.418 AC XY: 30992 AN XY: 74210

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.0247

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.431

Alfa AF: 0.502 Hom.: 7173

Bravo AF: 0.396

Asia WGS AF: 0.232 AC: 809 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.81
Dann	Benign	0.25

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: rs10797531; hg19: chr1-234276014;