rs1519860

Variant names:

• chr20-4942640-C-T
• rs1519860
• NM_005116.6:c.-154-9924G>A

Variant summary

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

The NM_005116.6(SLC23A2):​c.-154-9924G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,116 control chromosomes in the GnomAD database, including 1,351 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 0.11 (1351 hom., cov: 31)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.-154-9924G>A		intron_variant	Intron 2 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.-154-9924G>A		intron_variant	Intron 2 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.-154-9924G>A		intron_variant	Intron 2 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5	c.-154-9924G>A		intron_variant	Intron 2 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000468355.5	n.213-9924G>A		intron_variant	Intron 2 of 11	1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16756 AN: 151998 Hom.: 1345 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0456

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.110 AC: 16782 AN: 152116 Hom.: 1351 Cov.: 31 AF XY: 0.111 AC XY: 8222 AN XY: 74364

African (AFR) AF: 0.224 AC: 9299 AN: 41474

American (AMR) AF: 0.114 AC: 1748 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 359 AN: 3466

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5180

South Asian (SAS) AF: 0.120 AC: 580 AN: 4814

European-Finnish (FIN) AF: 0.0432 AC: 458 AN: 10598

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3853 AN: 67994

Other (OTH) AF: 0.101 AC: 214 AN: 2110

Alfa AF: 0.0966 Hom.: 344

Bravo AF: 0.118

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.43
PhyloP100		-0.33
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: rs1519860; hg19: chr20-4923286;