chr20-4889144-G-A

Variant names:

• chr20-4889144-G-A
• rs1629176
• NM_005116.6:c.483-3235C>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.483-3235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,052 control chromosomes in the GnomAD database, including 12,274 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 0.38 (12274 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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.483-3235C>T		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.483-3235C>T		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.483-3235C>T		intron	N/A	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.483-3235C>T		intron	N/A	ENSP00000368637.1
	SLC23A2	ENST00000468355.5	TSL:1	n.849-3235C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58233 AN: 151934 Hom.: 12276 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.383 AC: 58247 AN: 152052 Hom.: 12274 Cov.: 32 AF XY: 0.378 AC XY: 28084 AN XY: 74324

African (AFR) AF: 0.217 AC: 9018 AN: 41476

American (AMR) AF: 0.374 AC: 5720 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5168

South Asian (SAS) AF: 0.407 AC: 1960 AN: 4816

European-Finnish (FIN) AF: 0.394 AC: 4159 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33196 AN: 67974

Other (OTH) AF: 0.391 AC: 826 AN: 2110

Alfa AF: 0.455 Hom.: 9587

Bravo AF: 0.375

Asia WGS AF: 0.283 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.36
DANN	Benign	0.86
PhyloP100		-1.0
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: rs1629176; hg19: chr20-4869790;