rs6116558

Variant names:

• chr20-4864908-A-G
• rs6116558
• NM_005116.6:c.1357-2001T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005116.6(SLC23A2):​c.1357-2001T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,194 control chromosomes in the GnomAD database, including 3,601 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 0.18 (3601 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.1357-2001T>C		intron_variant	Intron 13 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.1357-2001T>C		intron_variant	Intron 13 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.1357-2001T>C		intron_variant	Intron 13 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5	c.1357-2001T>C		intron_variant	Intron 13 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000423430.1	c.625-2001T>C		intron_variant	Intron 5 of 7	5		ENSP00000396364.1

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28012 AN: 152076 Hom.: 3590 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.184 AC: 28060 AN: 152194 Hom.: 3601 Cov.: 32 AF XY: 0.183 AC XY: 13649 AN XY: 74426

African (AFR) AF: 0.365 AC: 15148 AN: 41478

American (AMR) AF: 0.119 AC: 1819 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5190

South Asian (SAS) AF: 0.0925 AC: 447 AN: 4832

European-Finnish (FIN) AF: 0.140 AC: 1488 AN: 10614

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8025 AN: 67996

Other (OTH) AF: 0.176 AC: 372 AN: 2114

Alfa AF: 0.150 Hom.: 5002

Bravo AF: 0.190

Asia WGS AF: 0.0560 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.75
PhyloP100		0.47
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: rs6116558; hg19: chr20-4845554;