NM_005116.6:c.109-6218G>C

Variant names:

• chr20-4919196-C-G
• rs1715366
• NM_005116.6:c.109-6218G>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.109-6218G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,098 control chromosomes in the GnomAD database, including 16,491 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 0.46 (16491 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.109-6218G>C		intron_variant	Intron 3 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.109-6218G>C		intron_variant	Intron 3 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.109-6218G>C		intron_variant	Intron 3 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5	c.109-6218G>C		intron_variant	Intron 3 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000468355.5	n.475-6218G>C		intron_variant	Intron 3 of 11	1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70220 AN: 151980 Hom.: 16470 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.462 AC: 70286 AN: 152098 Hom.: 16491 Cov.: 32 AF XY: 0.467 AC XY: 34684 AN XY: 74336

African (AFR) AF: 0.450 AC: 18677 AN: 41472

American (AMR) AF: 0.448 AC: 6852 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3361 AN: 5172

South Asian (SAS) AF: 0.473 AC: 2281 AN: 4826

European-Finnish (FIN) AF: 0.538 AC: 5692 AN: 10576

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30376 AN: 67978

Other (OTH) AF: 0.478 AC: 1011 AN: 2114

Alfa AF: 0.358 Hom.: 1179

Bravo AF: 0.455

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.14
DANN	Benign	0.44
PhyloP100		-2.5
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: rs1715366; hg19: chr20-4899842;