1-234288543-T-C

Position:

• chr1-234288543-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.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

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35F3	NM_173508.4	c.609-20558T>C		intron_variant		ENST00000366618.8	NP_775779.1
SLC35F3	NM_001300845.2	c.402-20558T>C		intron_variant			NP_001287774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35F3	ENST00000366618.8	c.609-20558T>C		intron_variant		2	NM_173508.4	ENSP00000355577.3
SLC35F3	ENST00000366617.3	c.402-20558T>C		intron_variant		1		ENSP00000355576.3

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

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.236

Alfa AF: 0.176 Hom.: 6100

Bravo AF: 0.232

Asia WGS AF: 0.529 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.78

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: rs542494; hg19: chr1-234424289; COSMIC: COSV64018812; COSMIC: COSV64018812;