rs1407149

Variant names:

• chr1-234317234-G-A
• rs1407149
• NM_173508.4:c.954+507G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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.954+507G>A		intron	N/A	NP_775779.1	Q8IY50-2
	SLC35F3	NM_001300845.2		c.747+507G>A		intron	N/A	NP_001287774.1	Q8IY50-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	ENST00000366618.8	TSL:2 MANE Select	c.954+507G>A		intron	N/A	ENSP00000355577.3	Q8IY50-2
	SLC35F3	ENST00000366617.3	TSL:1	c.747+507G>A		intron	N/A	ENSP00000355576.3	Q8IY50-1

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

African (AFR) AF: 0.148 AC: 6124 AN: 41494

American (AMR) AF: 0.0873 AC: 1335 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3470

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5180

South Asian (SAS) AF: 0.131 AC: 631 AN: 4818

European-Finnish (FIN) AF: 0.0847 AC: 897 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0778 AC: 5288 AN: 68006

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0858 Hom.: 2657

Bravo AF: 0.0993

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		0.11
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: rs1407149; hg19: chr1-234452980;