1-234288543-T-C

Variant names:

• chr1-234288543-T-C
• rs542494
• NM_173508.4:c.609-20558T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173508.4(SLC35F3):​c.609-20558T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,094 control chromosomes in the GnomAD database, including 5,119 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 0.22 (5119 hom., cov: 32)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973
• Publications: 3 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 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.609-20558T>C		intron	N/A	NP_775779.1	Q8IY50-2
	SLC35F3	NM_001300845.2		c.402-20558T>C		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.609-20558T>C		intron	N/A	ENSP00000355577.3	Q8IY50-2
	SLC35F3	ENST00000366617.3	TSL:1	c.402-20558T>C		intron	N/A	ENSP00000355576.3	Q8IY50-1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33870 AN: 151976 Hom.: 5105 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.223 AC: 33921 AN: 152094 Hom.: 5119 Cov.: 32 AF XY: 0.237 AC XY: 17641 AN XY: 74358

African (AFR) AF: 0.195 AC: 8094 AN: 41476

American (AMR) AF: 0.388 AC: 5939 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3466

East Asian (EAS) AF: 0.734 AC: 3785 AN: 5158

South Asian (SAS) AF: 0.413 AC: 1990 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2508 AN: 10572

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10308 AN: 68004

Other (OTH) AF: 0.236 AC: 496 AN: 2106

Alfa AF: 0.183 Hom.: 10755

Bravo AF: 0.232

Asia WGS AF: 0.529 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.97
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: rs542494; hg19: chr1-234424289; COSMIC: COSV64018812; COSMIC: COSV64018812;