rs16990309

Positions:

• chr20-4855794-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_005116.6(SLC23A2):​c.*1178G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,616 control chromosomes in the GnomAD database, including 11,425 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 0.29 (11423 hom., cov: 32)
  • Exomes 𝑓: 0.12 (2 hom.)
• Consequence: SLC23A2 NM_005116.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.777

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.*1178G>A		3_prime_UTR_variant	17/17	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.*1178G>A		3_prime_UTR_variant	17/17		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.*1178G>A		3_prime_UTR_variant	17/17	1	NM_005116.6	ENSP00000344322	P1
SLC23A2	ENST00000379333.5	c.*1178G>A		3_prime_UTR_variant	17/17	1		ENSP00000368637	P1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44545 AN: 152038 Hom.: 11372 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.117 AC: 54 AN: 460 Hom.: 2 Cov.: 0 AF XY: 0.137 AC XY: 38 AN XY: 278

Gnomad4 FIN exome AF: 0.114

Gnomad4 NFE exome AF: 0.0625

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.293 AC: 44652 AN: 152156 Hom.: 11423 Cov.: 32 AF XY: 0.290 AC XY: 21599 AN XY: 74400

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.264

Alfa AF: 0.179 Hom.: 3547

Bravo AF: 0.314

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Benign	0.89
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs16990309; hg19: chr20-4836440;