chr20-4961828-A-T

Variant names:

• chr20-4961828-A-T
• rs6139587
• NM_005116.6:c.-155+8965T>A

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+8965T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,066 control chromosomes in the GnomAD database, including 12,671 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 (12671 hom., cov: 32)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.54
• Publications: 4 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=-0.93).
• 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 rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.-155+8965T>A		intron_variant	Intron 2 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.-155+8965T>A		intron_variant	Intron 2 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.-155+8965T>A		intron_variant	Intron 2 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5	c.-155+8965T>A		intron_variant	Intron 2 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000468355.5	n.212+8965T>A		intron_variant	Intron 2 of 11	1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61321 AN: 151948 Hom.: 12652 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.404 AC: 61382 AN: 152066 Hom.: 12671 Cov.: 32 AF XY: 0.404 AC XY: 30064 AN XY: 74344

African (AFR) AF: 0.326 AC: 13513 AN: 41490

American (AMR) AF: 0.480 AC: 7323 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1581 AN: 3472

East Asian (EAS) AF: 0.383 AC: 1977 AN: 5160

South Asian (SAS) AF: 0.394 AC: 1902 AN: 4824

European-Finnish (FIN) AF: 0.443 AC: 4679 AN: 10572

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29041 AN: 67966

Other (OTH) AF: 0.397 AC: 837 AN: 2108

Alfa AF: 0.410 Hom.: 1780

Bravo AF: 0.407

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.023
DANN	Benign	0.56
PhyloP100		-4.5
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: rs6139587; hg19: chr20-4942474;