chr1-234321639-T-C

Variant names:

• chr1-234321639-T-C
• rs12118979
• NM_173508.4:c.1238-1369T>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.1238-1369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,204 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 31)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	NM_173508.4	MANE Select	c.1238-1369T>C		intron	N/A	NP_775779.1
	SLC35F3	NM_001300845.2		c.1031-1369T>C		intron	N/A	NP_001287774.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	ENST00000366618.8	TSL:2 MANE Select	c.1238-1369T>C		intron	N/A	ENSP00000355577.3
	SLC35F3	ENST00000366617.3	TSL:1	c.1031-1369T>C		intron	N/A	ENSP00000355576.3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16820 AN: 152086 Hom.: 1031 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.111 AC: 16859 AN: 152204 Hom.: 1040 Cov.: 31 AF XY: 0.110 AC XY: 8188 AN XY: 74434

African (AFR) AF: 0.150 AC: 6226 AN: 41506

American (AMR) AF: 0.103 AC: 1569 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 330 AN: 3470

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5182

South Asian (SAS) AF: 0.143 AC: 692 AN: 4828

European-Finnish (FIN) AF: 0.0949 AC: 1006 AN: 10604

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6667 AN: 68012

Other (OTH) AF: 0.107 AC: 226 AN: 2106

Alfa AF: 0.110 Hom.: 117

Bravo AF: 0.112

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.65
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs12118979; hg19: chr1-234457385;