rs1279683

Positions:

• chr20-5002446-G-A
• chr20-5002446-G-C

Variant summary

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

The ENST00000379333.5(SLC23A2):​c.-282+7736C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,960 control chromosomes in the GnomAD database, including 14,736 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 0.42 (14736 hom., cov: 32)
• Consequence: SLC23A2 ENST00000379333.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC23A2	NM_203327.2	c.-282+7736C>T		intron_variant			NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000379333.5	c.-282+7736C>T		intron_variant		1		ENSP00000368637	P1
SLC23A2	ENST00000468355.5	n.89+7736C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63534 AN: 151842 Hom.: 14727 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.418 AC: 63564 AN: 151960 Hom.: 14736 Cov.: 32 AF XY: 0.415 AC XY: 30851 AN XY: 74284

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.409

Alfa AF: 0.294 Hom.: 1508

Bravo AF: 0.431

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1279683; hg19: chr20-4983092;