dbSNP rs6139591: SLC23A2:c.-155+80C>T (chr20-4970713-G-A) – 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+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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Publications

8 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:

Genome browser will be placed here

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=-0.91).

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 link	c.-155+80C>T		intron_variant	Intron 2 of 16	ENST00000338244.6	NP_005107.4
SLC23A2	NM_203327.2 link	c.-155+80C>T		intron_variant	Intron 2 of 16		NP_976072.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
SLC23A2	ENST00000338244.6 link	c.-155+80C>T	intron_variant	Intron 2 of 16	1	NM_005116.6	ENSP00000344322.1
SLC23A2	ENST00000379333.5 link	c.-155+80C>T	intron_variant	Intron 2 of 16	1		ENSP00000368637.1
SLC23A2	ENST00000468355.5 link	n.212+80C>T	intron_variant	Intron 2 of 11	1

Frequencies

GnomAD3 genomes

AF:

0.403

AC:

61281

AN:

152028

Hom.:

12609

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.452

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.391

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.403

AC:

61333

AN:

152146

Hom.:

12620

Cov.:

AF XY:

0.402

AC XY:

29912

AN XY:

74360

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.423

AC:

28801

AN:

68020

Other (OTH)

AF:

0.395

AC:

835

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1899

3798

5698

7597

9496

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.401

Hom.:

1548

Bravo

AF:

0.409

Asia WGS

AF:

0.417

AC:

1450

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

(source)

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)

(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