rs1715385

Variant names:

• chr20-4907024-G-A
• rs1715385
• NM_005116.6:c.208-4466C>T

Variant summary

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

The NM_005116.6(SLC23A2):​c.208-4466C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,930 control chromosomes in the GnomAD database, including 19,641 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 0.51 (19641 hom., cov: 31)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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.208-4466C>T		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.208-4466C>T		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.208-4466C>T		intron	N/A	ENSP00000344322.1	Q9UGH3-1
	SLC23A2	ENST00000379333.5	TSL:1	c.208-4466C>T		intron	N/A	ENSP00000368637.1	Q9UGH3-1
	SLC23A2	ENST00000468355.5	TSL:1	n.574-4466C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76864 AN: 151812 Hom.: 19635 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.506 AC: 76898 AN: 151930 Hom.: 19641 Cov.: 31 AF XY: 0.511 AC XY: 37924 AN XY: 74252

African (AFR) AF: 0.477 AC: 19761 AN: 41434

American (AMR) AF: 0.498 AC: 7593 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3468

East Asian (EAS) AF: 0.530 AC: 2742 AN: 5176

South Asian (SAS) AF: 0.470 AC: 2263 AN: 4820

European-Finnish (FIN) AF: 0.627 AC: 6616 AN: 10548

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34849 AN: 67922

Other (OTH) AF: 0.513 AC: 1081 AN: 2108

Alfa AF: 0.504 Hom.: 34332

Bravo AF: 0.492

Asia WGS AF: 0.484 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.37
PhyloP100		-0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1715385; hg19: chr20-4887670;