rs6052937

Positions:

• chr20-4854692-C-A

Variant summary

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

The NM_005116.6(SLC23A2):​c.*2280G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,104 control chromosomes in the GnomAD database, including 15,014 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 0.34 (15013 hom., cov: 32)
  • Exomes 𝑓: 0.24 (1 hom.)
• Consequence: SLC23A2 NM_005116.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC23A2	NM_005116.6	c.*2280G>T		3_prime_UTR_variant	17/17	ENST00000338244.6
SLC23A2	NM_203327.2	c.*2280G>T		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC23A2	ENST00000338244.6	c.*2280G>T		3_prime_UTR_variant	17/17	1	NM_005116.6	P1
SLC23A2	ENST00000379333.5	c.*2280G>T		3_prime_UTR_variant	17/17	1		P1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50842 AN: 151946 Hom.: 14962 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.237 AC: 9 AN: 38 Hom.: 1 Cov.: 0 AF XY: 0.167 AC XY: 4 AN XY: 24

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.335 AC: 50951 AN: 152066 Hom.: 15013 Cov.: 32 AF XY: 0.330 AC XY: 24544 AN XY: 74352

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.313

Alfa AF: 0.174 Hom.: 7436

Bravo AF: 0.360

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.52

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: rs6052937; hg19: chr20-4835338;