rs6133175

Variant names:

• chr20-4911113-A-G
• rs6133175
• NM_005116.6:c.207+1767T>C

Variant summary

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

The NM_005116.6(SLC23A2):​c.207+1767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,034 control chromosomes in the GnomAD database, including 7,990 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 0.29 (7990 hom., cov: 31)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 18 publications found

Genes affected

SLC23A2 (HGNC:10973): (solute carrier family 23 member 2) The absorption of vitamin C into the body and its distribution to organs requires two sodium-dependent vitamin C transporters. This gene encodes one of the two required transporters and the encoded protein accounts for tissue-specific uptake of vitamin C. Previously, this gene had an official symbol of SLC23A1. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005116.6. 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
	SLC23A2	NM_005116.6	MANE Select	c.207+1767T>C		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.207+1767T>C		intron	N/A	NP_976072.1	Q9UGH3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	ENST00000338244.6	TSL:1 MANE Select	c.207+1767T>C		intron	N/A	ENSP00000344322.1	Q9UGH3-1
	SLC23A2	ENST00000379333.5	TSL:1	c.207+1767T>C		intron	N/A	ENSP00000368637.1	Q9UGH3-1
	SLC23A2	ENST00000468355.5	TSL:1	n.573+1767T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44216 AN: 151916 Hom.: 7984 Cov.: 31

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.291 AC: 44231 AN: 152034 Hom.: 7990 Cov.: 31 AF XY: 0.300 AC XY: 22295 AN XY: 74304

African (AFR) AF: 0.0879 AC: 3650 AN: 41524

American (AMR) AF: 0.342 AC: 5225 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3466

East Asian (EAS) AF: 0.636 AC: 3274 AN: 5148

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4814

European-Finnish (FIN) AF: 0.481 AC: 5080 AN: 10556

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23379 AN: 67942

Other (OTH) AF: 0.313 AC: 660 AN: 2112

Alfa AF: 0.322 Hom.: 24909

Bravo AF: 0.275

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.0
DANN	Benign	0.78
PhyloP100		1.6
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: rs6133175; hg19: chr20-4891759;