20-4929943-G-C

Variant names:

• chr20-4929943-G-C
• rs1715372
• NM_005116.6:c.108+2512C>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.108+2512C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,998 control chromosomes in the GnomAD database, including 25,047 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 0.56 (25047 hom., cov: 31)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.108+2512C>G		intron_variant	Intron 3 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.108+2512C>G		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.108+2512C>G		intron_variant	Intron 3 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5	c.108+2512C>G		intron_variant	Intron 3 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000468355.5	n.474+2512C>G		intron_variant	Intron 3 of 11	1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84961 AN: 151880 Hom.: 25013 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.560 AC: 85049 AN: 151998 Hom.: 25047 Cov.: 31 AF XY: 0.564 AC XY: 41913 AN XY: 74282

African (AFR) AF: 0.740 AC: 30683 AN: 41474

American (AMR) AF: 0.546 AC: 8337 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1690 AN: 3466

East Asian (EAS) AF: 0.705 AC: 3634 AN: 5156

South Asian (SAS) AF: 0.543 AC: 2611 AN: 4810

European-Finnish (FIN) AF: 0.545 AC: 5759 AN: 10558

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

European-Non Finnish (NFE) AF: 0.453 AC: 30771 AN: 67936

Other (OTH) AF: 0.550 AC: 1161 AN: 2112

Alfa AF: 0.389 Hom.: 1228

Bravo AF: 0.565

Asia WGS AF: 0.642 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.82
PhyloP100		0.20
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: rs1715372; hg19: chr20-4910589;