chr20-4918250-T-C

Variant names:

• chr20-4918250-T-C
• rs1715364
• NM_005116.6:c.109-5272A>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.109-5272A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,040 control chromosomes in the GnomAD database, including 24,524 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 0.55 (24524 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	NM_005116.6	MANE Select	c.109-5272A>G		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.109-5272A>G		intron	N/A	NP_976072.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	ENST00000338244.6	TSL:1 MANE Select	c.109-5272A>G		intron	N/A	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.109-5272A>G		intron	N/A	ENSP00000368637.1
	SLC23A2	ENST00000468355.5	TSL:1	n.475-5272A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83899 AN: 151922 Hom.: 24479 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.552 AC: 83995 AN: 152040 Hom.: 24524 Cov.: 32 AF XY: 0.554 AC XY: 41194 AN XY: 74318

African (AFR) AF: 0.748 AC: 31010 AN: 41476

American (AMR) AF: 0.493 AC: 7530 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3359 AN: 5160

South Asian (SAS) AF: 0.474 AC: 2289 AN: 4826

European-Finnish (FIN) AF: 0.544 AC: 5737 AN: 10554

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30814 AN: 67978

Other (OTH) AF: 0.543 AC: 1144 AN: 2108

Alfa AF: 0.473 Hom.: 27639

Bravo AF: 0.556

Asia WGS AF: 0.587 AC: 2040 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.32
PhyloP100		-2.7
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: rs1715364; hg19: chr20-4898896;