rs12479919

chr20-5000094-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005116.6(SLC23A2):c.-282+1312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,910 control chromosomes in the GnomAD database, including 8,713 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 0.32 (8713 hom., cov: 31)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC23A2	NM_005116.6	c.-282+1312G>A		intron_variant		ENST00000338244.6
SLC23A2	NM_203327.2	c.-282+10088G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC23A2	ENST00000338244.6	c.-282+1312G>A		intron_variant		1	NM_005116.6	P1
SLC23A2	ENST00000379333.5	c.-282+10088G>A		intron_variant		1		P1
SLC23A2	ENST00000468355.5	n.89+10088G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48998 AN: 151792 Hom.: 8706 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.323 AC: 49023 AN: 151910 Hom.: 8713 Cov.: 31 AF XY: 0.325 AC XY: 24110 AN XY: 74252

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.310

Alfa AF: 0.366 Hom.: 4681

Bravo AF: 0.316

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	11
Dann	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs12479919; hg19: chr20-4980740;