NM_005116.6:c.-282+14050C>A

Variant names:

• chr20-4987356-G-T
• rs2681118
• NM_005116.6:c.-282+14050C>A

Variant summary

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

The NM_005116.6(SLC23A2):​c.-282+14050C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,094 control chromosomes in the GnomAD database, including 52,146 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 0.83 (52146 hom., cov: 31)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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.-282+14050C>A		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.-281-16437C>A		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.-282+14050C>A		intron	N/A	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.-281-16437C>A		intron	N/A	ENSP00000368637.1
	SLC23A2	ENST00000468355.5	TSL:1	n.90-16441C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125725 AN: 151976 Hom.: 52097 Cov.: 31

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.827 AC: 125835 AN: 152094 Hom.: 52146 Cov.: 31 AF XY: 0.829 AC XY: 61616 AN XY: 74344

African (AFR) AF: 0.773 AC: 32075 AN: 41496

American (AMR) AF: 0.843 AC: 12862 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3000 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5095 AN: 5182

South Asian (SAS) AF: 0.851 AC: 4100 AN: 4820

European-Finnish (FIN) AF: 0.870 AC: 9206 AN: 10576

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56783 AN: 67982

Other (OTH) AF: 0.821 AC: 1734 AN: 2112

Alfa AF: 0.800 Hom.: 2629

Bravo AF: 0.825

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.55
PhyloP100		-1.8
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: rs2681118; hg19: chr20-4968002;