20-4876098-A-G

Variant names:

• chr20-4876098-A-G
• rs6107546
• NM_005116.6:c.825-1402T>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.825-1402T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,192 control chromosomes in the GnomAD database, including 2,494 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 0.16 (2494 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.825-1402T>C		intron_variant	Intron 9 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.825-1402T>C		intron_variant	Intron 9 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.825-1402T>C		intron_variant	Intron 9 of 16	1	NM_005116.6	ENSP00000344322.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24947 AN: 152074 Hom.: 2484 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 25002 AN: 152192 Hom.: 2494 Cov.: 32 AF XY: 0.164 AC XY: 12192 AN XY: 74412

African (AFR) AF: 0.274 AC: 11381 AN: 41490

American (AMR) AF: 0.118 AC: 1801 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5188

South Asian (SAS) AF: 0.112 AC: 539 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8540 AN: 68016

Other (OTH) AF: 0.163 AC: 345 AN: 2112

Alfa AF: 0.132 Hom.: 2522

Bravo AF: 0.166

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6107546; hg19: chr20-4856744;