20-4884071-T-C

Variant names:

• chr20-4884071-T-C
• rs6116569
• NM_005116.6:c.643-248A>G

Variant summary

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

The NM_005116.6(SLC23A2):​c.643-248A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,068 control chromosomes in the GnomAD database, including 32,794 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 0.63 (32794 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	NM_005116.6	MANE Select	c.643-248A>G		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.643-248A>G		intron	N/A	NP_976072.1	Q9UGH3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	ENST00000338244.6	TSL:1 MANE Select	c.643-248A>G		intron	N/A	ENSP00000344322.1	Q9UGH3-1
	SLC23A2	ENST00000379333.5	TSL:1	c.643-248A>G		intron	N/A	ENSP00000368637.1	Q9UGH3-1
	SLC23A2	ENST00000468355.5	TSL:1	n.1009-248A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95696 AN: 151950 Hom.: 32740 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.630 AC: 95797 AN: 152068 Hom.: 32794 Cov.: 32 AF XY: 0.621 AC XY: 46120 AN XY: 74318

African (AFR) AF: 0.905 AC: 37572 AN: 41506

American (AMR) AF: 0.514 AC: 7859 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2159 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1332 AN: 5174

South Asian (SAS) AF: 0.514 AC: 2476 AN: 4816

European-Finnish (FIN) AF: 0.428 AC: 4523 AN: 10558

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37853 AN: 67950

Other (OTH) AF: 0.621 AC: 1312 AN: 2112

Alfa AF: 0.574 Hom.: 32399

Bravo AF: 0.648

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.58
PhyloP100		-0.21
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: rs6116569; hg19: chr20-4864717;