rs1407149

chr1-234317234-G-A

Variant summary

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

The NM_173508.4(SLC35F3):c.954+507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 152,170 control chromosomes in the GnomAD database, including 850 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 0.097 (850 hom., cov: 32)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F3	NM_173508.4	c.954+507G>A		intron_variant		ENST00000366618.8
SLC35F3	NM_001300845.2	c.747+507G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F3	ENST00000366618.8	c.954+507G>A		intron_variant		2	NM_173508.4
SLC35F3	ENST00000366617.3	c.747+507G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0973 AC: 14801 AN: 152052 Hom.: 842 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0975 AC: 14836 AN: 152170 Hom.: 850 Cov.: 32 AF XY: 0.0967 AC XY: 7192 AN XY: 74386

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0873

Gnomad4 ASJ AF: 0.0735

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0847

Gnomad4 NFE AF: 0.0778

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0826 Hom.: 1125

Bravo AF: 0.0993

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.5
Dann	Benign	0.58

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: rs1407149; hg19: chr1-234452980;