rs13037458

Variant names:

• chr20-4970569-A-C
• rs13037458
• NM_005116.6:c.-155+224T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-4970569-A-C
• chr20-4970569-A-T

Variant summary

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

The NM_005116.6(SLC23A2):​c.-155+224T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,674 control chromosomes in the GnomAD database, including 14,878 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 0.44 (14878 hom., cov: 30)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28
• Publications: 5 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=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	NM_005116.6	MANE Select	c.-155+224T>G		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.-155+224T>G		intron	N/A	NP_976072.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	ENST00000338244.6	TSL:1 MANE Select	c.-155+224T>G		intron	N/A	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.-155+224T>G		intron	N/A	ENSP00000368637.1
	SLC23A2	ENST00000468355.5	TSL:1	n.212+224T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 66938 AN: 151558 Hom.: 14868 Cov.: 30

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.442 AC: 66993 AN: 151674 Hom.: 14878 Cov.: 30 AF XY: 0.442 AC XY: 32763 AN XY: 74106

African (AFR) AF: 0.445 AC: 18413 AN: 41356

American (AMR) AF: 0.493 AC: 7507 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1524 AN: 3462

East Asian (EAS) AF: 0.439 AC: 2257 AN: 5136

South Asian (SAS) AF: 0.527 AC: 2526 AN: 4792

European-Finnish (FIN) AF: 0.418 AC: 4402 AN: 10522

Middle Eastern (MID) AF: 0.334 AC: 97 AN: 290

European-Non Finnish (NFE) AF: 0.426 AC: 28928 AN: 67878

Other (OTH) AF: 0.434 AC: 914 AN: 2104

Alfa AF: 0.253 Hom.: 527

Bravo AF: 0.448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.59
PhyloP100		-3.3
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: rs13037458; hg19: chr20-4951215;