chr20-4853692-C-T

Position:

• chr20-4853692-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_005116.6(SLC23A2):​c.*3280G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,432 control chromosomes in the GnomAD database, including 24,084 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 (24044 hom., cov: 32)
  • Exomes 𝑓: 0.43 (40 hom.)
• Consequence: SLC23A2 NM_005116.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC23A2	NM_005116.6	c.*3280G>A		3_prime_UTR_variant	17/17	ENST00000338244.6
SLC23A2	NM_203327.2	c.*3280G>A		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC23A2	ENST00000338244.6	c.*3280G>A		3_prime_UTR_variant	17/17	1	NM_005116.6	P1
SLC23A2	ENST00000379333.5	c.*3280G>A		3_prime_UTR_variant	17/17	1		P1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83640 AN: 151912 Hom.: 24011 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.565

GnomAD4 exome AF: 0.431 AC: 174 AN: 404 Hom.: 40 Cov.: 0 AF XY: 0.416 AC XY: 99 AN XY: 238

Gnomad4 FIN exome AF: 0.432

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.551 AC: 83723 AN: 152028 Hom.: 24044 Cov.: 32 AF XY: 0.545 AC XY: 40489 AN XY: 74332

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.568

Alfa AF: 0.515 Hom.: 28404

Bravo AF: 0.564

Asia WGS AF: 0.530 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	13
DANN	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs1131382; hg19: chr20-4834338;