chr20-4970713-G-A

Variant names:

• chr20-4970713-G-A
• rs6139591
• NM_005116.6:c.-155+80C>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.-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
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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.-155+80C>T		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.-155+80C>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.-155+80C>T		intron	N/A	ENSP00000344322.1
	SLC23A2	ENST00000379333.5	TSL:1	c.-155+80C>T		intron	N/A	ENSP00000368637.1
	SLC23A2	ENST00000468355.5	TSL:1	n.212+80C>T		intron	N/A

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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 0.250 AC: 1 AN: 4

European-Non Finnish (NFE) AF: 0.391 AC: 18 AN: 46

Other (OTH) AF: 0.333 AC: 2 AN: 6

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

African (AFR) AF: 0.338 AC: 14042 AN: 41494

American (AMR) AF: 0.479 AC: 7323 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1525 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1991 AN: 5172

South Asian (SAS) AF: 0.388 AC: 1867 AN: 4816

European-Finnish (FIN) AF: 0.419 AC: 4423 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28801 AN: 68020

Other (OTH) AF: 0.395 AC: 835 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs6139591; hg19: chr20-4951359;