NM_173508.4:c.284-95816T>C

Variant names:

• chr1-234135601-T-C
• rs1463502
• NM_173508.4:c.284-95816T>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.284-95816T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,096 control chromosomes in the GnomAD database, including 6,014 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 0.24 (6014 hom., cov: 32)
• Consequence: SLC35F3 NM_173508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 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.284-95816T>C		intron	N/A	NP_775779.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F3	ENST00000366618.8	TSL:2 MANE Select	c.284-95816T>C		intron	N/A	ENSP00000355577.3

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36647 AN: 151978 Hom.: 6000 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.241 AC: 36705 AN: 152096 Hom.: 6014 Cov.: 32 AF XY: 0.247 AC XY: 18350 AN XY: 74334

African (AFR) AF: 0.356 AC: 14769 AN: 41480

American (AMR) AF: 0.295 AC: 4501 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3464

East Asian (EAS) AF: 0.747 AC: 3845 AN: 5146

South Asian (SAS) AF: 0.287 AC: 1384 AN: 4820

European-Finnish (FIN) AF: 0.147 AC: 1560 AN: 10586

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9380 AN: 68004

Other (OTH) AF: 0.240 AC: 508 AN: 2116

Alfa AF: 0.171 Hom.: 4345

Bravo AF: 0.264

Asia WGS AF: 0.476 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.68
PhyloP100		-1.3
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: rs1463502; hg19: chr1-234271347;