rs8126036

chr20-4883297-T-C

Variant summary

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

The NM_005116.6(SLC23A2):c.824+345A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 152,186 control chromosomes in the GnomAD database, including 617 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 0.061 (617 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC23A2	NM_005116.6	c.824+345A>G		intron_variant		ENST00000338244.6
SLC23A2	NM_203327.2	c.824+345A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC23A2	ENST00000338244.6	c.824+345A>G		intron_variant		1	NM_005116.6	P1

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9230 AN: 152068 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0409

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0608 AC: 9250 AN: 152186 Hom.: 617 Cov.: 32 AF XY: 0.0599 AC XY: 4456 AN XY: 74406

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0372

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.00631

Gnomad4 NFE AF: 0.0189

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0344 Hom.: 80

Bravo AF: 0.0659

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	10
Dann	Benign	0.86

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: rs8126036; hg19: chr20-4863943;