rs6052937

Variant names:

• chr20-4854692-C-A
• rs6052937
• NM_005116.6:c.*2280G>T

Variant summary

Our verdict is Benign. The variant received -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. Variant has been reported in ClinVar as (no stars).

• 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
• Publications: 13 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 -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.

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.*2280G>T		3_prime_UTR	Exon 17 of 17	NP_005107.4
	SLC23A2	NM_203327.2		c.*2280G>T		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.*2280G>T		3_prime_UTR	Exon 17 of 17	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.*2280G>T		3_prime_UTR	Exon 17 of 17	ENSP00000368637.1
	SLC23A2	ENST00000877970.1		c.*2280G>T		3_prime_UTR	Exon 19 of 19	ENSP00000548029.1

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.150 AC: 3 AN: 20

Other (OTH) AF: 0.667 AC: 4 AN: 6

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

African (AFR) AF: 0.805 AC: 33348 AN: 41446

American (AMR) AF: 0.215 AC: 3279 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3468

East Asian (EAS) AF: 0.110 AC: 566 AN: 5168

South Asian (SAS) AF: 0.217 AC: 1044 AN: 4814

European-Finnish (FIN) AF: 0.131 AC: 1392 AN: 10600

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9643 AN: 67976

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.207 Hom.: 18021

Bravo AF: 0.360

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		0.010
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: rs6052937; hg19: chr20-4835338;