rs6139591

chr20-4970713-G-Achr20-4970713-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005116.6(SLC23A2):c.-155+80C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,212 control chromosomes in the GnomAD database, including 12,627 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 0.40 (12620 hom., cov: 33)
  • Exomes 𝑓: 0.41 (7 hom.)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC23A2	NM_005116.6	c.-155+80C>T		intron_variant		ENST00000338244.6
SLC23A2	NM_203327.2	c.-155+80C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC23A2	ENST00000338244.6	c.-155+80C>T		intron_variant		1	NM_005116.6	P1
SLC23A2	ENST00000379333.5	c.-155+80C>T		intron_variant		1		P1
SLC23A2	ENST00000468355.5	n.212+80C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61281 AN: 152028 Hom.: 12609 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.391

GnomAD4 exome AF: 0.409 AC: 27 AN: 66 Hom.: 7 AF XY: 0.452 AC XY: 19 AN XY: 42

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.391

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.403 AC: 61333 AN: 152146 Hom.: 12620 Cov.: 33 AF XY: 0.402 AC XY: 29912 AN XY: 74360

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.395

Alfa AF: 0.401 Hom.: 1548

Bravo AF: 0.409

Asia WGS AF: 0.417 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs6139591; hg19: chr20-4951359;