rs16990309

Variant names:

• chr20-4855794-C-T
• rs16990309
• NM_005116.6:c.*1178G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005116.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	NM_005116.6	MANE Select	c.*1178G>A		3_prime_UTR	Exon 17 of 17	NP_005107.4
	SLC23A2	NM_203327.2		c.*1178G>A		3_prime_UTR	Exon 17 of 17	NP_976072.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	ENST00000338244.6	TSL:1 MANE Select	c.*1178G>A		3_prime_UTR	Exon 17 of 17	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.*1178G>A		3_prime_UTR	Exon 17 of 17	ENSP00000368637.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.114 AC: 50 AN: 438

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0625 AC: 1 AN: 16

Other (OTH) AF: 0.500 AC: 3 AN: 6

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

African (AFR) AF: 0.698 AC: 28965 AN: 41488

American (AMR) AF: 0.207 AC: 3157 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3472

East Asian (EAS) AF: 0.101 AC: 521 AN: 5180

South Asian (SAS) AF: 0.183 AC: 886 AN: 4830

European-Finnish (FIN) AF: 0.119 AC: 1257 AN: 10580

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8707 AN: 68000

Other (OTH) AF: 0.264 AC: 559 AN: 2116

Alfa AF: 0.232 Hom.: 8920

Bravo AF: 0.314

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Benign	0.89
PhyloP100		0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16990309; hg19: chr20-4836440;