chr20-5000094-C-T

Variant names:

• chr20-5000094-C-T
• rs12479919
• NM_005116.6:c.-282+1312G>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.-282+1312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,910 control chromosomes in the GnomAD database, including 8,713 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 0.32 (8713 hom., cov: 31)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 15 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.-282+1312G>A		intron_variant	Intron 1 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.-282+10088G>A		intron_variant	Intron 1 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.-282+1312G>A		intron_variant	Intron 1 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5	c.-282+10088G>A		intron_variant	Intron 1 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000468355.5	n.89+10088G>A		intron_variant	Intron 1 of 11	1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48998 AN: 151792 Hom.: 8706 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.323 AC: 49023 AN: 151910 Hom.: 8713 Cov.: 31 AF XY: 0.325 AC XY: 24110 AN XY: 74252

African (AFR) AF: 0.163 AC: 6742 AN: 41464

American (AMR) AF: 0.401 AC: 6117 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1732 AN: 5152

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4812

European-Finnish (FIN) AF: 0.429 AC: 4522 AN: 10538

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25913 AN: 67924

Other (OTH) AF: 0.310 AC: 652 AN: 2104

Alfa AF: 0.364 Hom.: 5204

Bravo AF: 0.316

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		0.35
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: rs12479919; hg19: chr20-4980740;