Genetic Variant NM_005116.6:c.*3280G>A (chr20-4853692-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_005116.6(SLC23A2):c.*3280G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,432 control chromosomes in the GnomAD database, including 24,084 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 0.55 ( 24044 hom., cov: 32)

Exomes 𝑓: 0.43 ( 40 hom. )

Consequence

SLC23A2
NM_005116.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.462

Publications

11 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC23A2	NM_005116.6 link	c.*3280G>A		3_prime_UTR_variant	Exon 17 of 17	ENST00000338244.6	NP_005107.4	Q9UGH3-1A0A140VK48
SLC23A2	NM_203327.2 link	c.*3280G>A		3_prime_UTR_variant	Exon 17 of 17		NP_976072.1	Q9UGH3-1A0A140VK48

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC23A2	ENST00000338244.6 link	c.*3280G>A		3_prime_UTR_variant	Exon 17 of 17	1	NM_005116.6	ENSP00000344322.1		Q9UGH3-1
SLC23A2	ENST00000379333.5 link	c.*3280G>A		3_prime_UTR_variant	Exon 17 of 17	1		ENSP00000368637.1		Q9UGH3-1

Frequencies

GnomAD3 genomes

AF:

0.551

AC:

83640

AN:

151912

Hom.:

24011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.711

Gnomad AMI

AF:

0.533

Gnomad AMR

AF:

0.495

Gnomad ASJ

AF:

0.652

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.384

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.565

GnomAD4 exome

AF:

0.431

AC:

174

AN:

404

Hom.:

Cov.:

AF XY:

0.416

AC XY:

AN XY:

238

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:

0.432

AC:

173

AN:

400

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.551

AC:

83723

AN:

152028

Hom.:

24044

Cov.:

AF XY:

0.545

AC XY:

40489

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.712

AC:

29500

AN:

41456

American (AMR)

AF:

0.495

AC:

7559

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.652

AC:

2263

AN:

3470

East Asian (EAS)

AF:

0.542

AC:

2806

AN:

5176

South Asian (SAS)

AF:

0.469

AC:

2261

AN:

4822

European-Finnish (FIN)

AF:

0.384

AC:

4055

AN:

10568

Middle Eastern (MID)

AF:

0.633

AC:

186

AN:

294

European-Non Finnish (NFE)

AF:

0.492

AC:

33416

AN:

67956

Other (OTH)

AF:

0.568

AC:

1196

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1849

3697

5546

7394

9243

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

714

1428

2142

2856

3570

<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:

0.520

Hom.:

39708

Bravo

AF:

0.564

Asia WGS

AF:

0.530

AC:

1845

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

0.46

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over