20-4883924-G-C

Variant names:

• chr20-4883924-G-C
• rs2298174
• NM_005116.6:c.643-101C>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.643-101C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 840,106 control chromosomes in the GnomAD database, including 37,077 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 0.27 (5814 hom., cov: 32)
  • Exomes 𝑓: 0.30 (31263 hom.)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 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.643-101C>G		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.643-101C>G		intron	N/A	NP_976072.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC23A2	ENST00000338244.6	TSL:1 MANE Select	c.643-101C>G		intron	N/A	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.643-101C>G		intron	N/A	ENSP00000368637.1
	SLC23A2	ENST00000468355.5	TSL:1	n.1009-101C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41455 AN: 152026 Hom.: 5811 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.299 AC: 205914 AN: 687962 Hom.: 31263 AF XY: 0.301 AC XY: 105982 AN XY: 351622

African (AFR) AF: 0.230 AC: 3611 AN: 15690

American (AMR) AF: 0.259 AC: 4667 AN: 18048

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 3939 AN: 14330

East Asian (EAS) AF: 0.199 AC: 5876 AN: 29590

South Asian (SAS) AF: 0.342 AC: 15934 AN: 46552

European-Finnish (FIN) AF: 0.255 AC: 9438 AN: 36944

Middle Eastern (MID) AF: 0.309 AC: 1218 AN: 3944

European-Non Finnish (NFE) AF: 0.310 AC: 151534 AN: 489586

Other (OTH) AF: 0.291 AC: 9697 AN: 33278

GnomAD4 genome AF: 0.273 AC: 41487 AN: 152144 Hom.: 5814 Cov.: 32 AF XY: 0.272 AC XY: 20249 AN XY: 74384

African (AFR) AF: 0.226 AC: 9361 AN: 41502

American (AMR) AF: 0.252 AC: 3848 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1181 AN: 5176

South Asian (SAS) AF: 0.336 AC: 1622 AN: 4824

European-Finnish (FIN) AF: 0.273 AC: 2891 AN: 10578

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20637 AN: 67994

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.167 Hom.: 353

Bravo AF: 0.271

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.16
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: rs2298174; hg19: chr20-4864570; COSMIC: COSV57775913;