chr20-4899545-C-T

Variant names:

• chr20-4899545-C-T
• rs202059859
• NM_005116.6:c.482+10G>A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_005116.6(SLC23A2):​c.482+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00225 in 1,613,944 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0017 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0023 (13 hom.)
• Consequence: SLC23A2 NM_005116.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.33

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 20-4899545-C-T is Benign according to our data. Variant chr20-4899545-C-T is described in ClinVar as [Benign]. Clinvar id is 791436.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 261 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6	c.482+10G>A		intron_variant	Intron 6 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2	c.482+10G>A		intron_variant	Intron 6 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6	c.482+10G>A		intron_variant	Intron 6 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5	c.482+10G>A		intron_variant	Intron 6 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000468355.5	n.848+10G>A		intron_variant	Intron 6 of 11	1
SLC23A2	ENST00000423430.1	c.92+10G>A		intron_variant	Intron 1 of 7	5		ENSP00000396364.1

Frequencies

GnomAD3 genomes AF: 0.00172 AC: 261 AN: 152186 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000410

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00209

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00273

Gnomad OTH AF: 0.000956

GnomAD3 exomes AF: 0.00171 AC: 430 AN: 251292 Hom.: 1 AF XY: 0.00160 AC XY: 217 AN XY: 135802

Gnomad AFR exome AF: 0.000308

Gnomad AMR exome AF: 0.00124

Gnomad ASJ exome AF: 0.00657

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000509

Gnomad NFE exome AF: 0.00254

Gnomad OTH exome AF: 0.00261

GnomAD4 exome AF: 0.00231 AC: 3372 AN: 1461640 Hom.: 13 Cov.: 34 AF XY: 0.00223 AC XY: 1624 AN XY: 727120

Gnomad4 AFR exome AF: 0.000269

Gnomad4 AMR exome AF: 0.00127

Gnomad4 ASJ exome AF: 0.00666

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00129

Gnomad4 NFE exome AF: 0.00260

Gnomad4 OTH exome AF: 0.00277

GnomAD4 genome AF: 0.00171 AC: 261 AN: 152304 Hom.: 0 Cov.: 32 AF XY: 0.00156 AC XY: 116 AN XY: 74484

Gnomad4 AFR AF: 0.000409

Gnomad4 AMR AF: 0.00209

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00273

Gnomad4 OTH AF: 0.000946

Alfa AF: 0.00264 Hom.: 1

Bravo AF: 0.00186

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 31, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	17
DANN	Benign	0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.30		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.30		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs202059859; hg19: chr20-4880191;