Genetic Variant SLC23A2:c.-155+108A>G (chr20-4970685-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005116.6(SLC23A2):c.-155+108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,170 control chromosomes in the GnomAD database, including 26,032 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 0.58 ( 26032 hom., cov: 33)

Exomes 𝑓: 0.48 ( 8 hom. )

Failed GnomAD Quality Control

Consequence

SLC23A2
NM_005116.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.39

Publications

5 publications found

Variant links:

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]

SLC23A2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 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+108A>G		intron	N/A	NP_005107.4
	SLC23A2	NM_203327.2		c.-155+108A>G		intron	N/A	NP_976072.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC23A2	ENST00000338244.6	TSL:1 MANE Select	c.-155+108A>G	intron	N/A	ENSP00000344322.1
SLC23A2	ENST00000379333.5	TSL:1	c.-155+108A>G	intron	N/A	ENSP00000368637.1
SLC23A2	ENST00000468355.5	TSL:1	n.212+108A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88611

AN:

152052

Hom.:

26006

Cov.:

show subpopulations

Gnomad AFR

AF:

0.627

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.604

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.454

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.531

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.570

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.481

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.476

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.583

AC:

88690

AN:

152170

Hom.:

26032

Cov.:

AF XY:

0.582

AC XY:

43319

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.627

AC:

26004

AN:

41502

American (AMR)

AF:

0.604

AC:

9238

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

2103

AN:

3470

East Asian (EAS)

AF:

0.454

AC:

2352

AN:

5178

South Asian (SAS)

AF:

0.674

AC:

3250

AN:

4824

European-Finnish (FIN)

AF:

0.531

AC:

5611

AN:

10568

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.562

AC:

38205

AN:

68022

Other (OTH)

AF:

0.571

AC:

1207

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1961

3922

5882

7843

9804

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.563

Hom.:

3006

Bravo

AF:

0.587

Asia WGS

AF:

0.579

AC:

2014

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.18

(source)

DANN

Benign

0.25

PhyloP100

-2.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over