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GeneBe

20-4912913-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_005116.6(SLC23A2):c.174G>A(p.Ala58=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00231 in 1,607,208 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.012 ( 37 hom., cov: 30)
Exomes 𝑓: 0.0014 ( 31 hom. )

Consequence

SLC23A2
NM_005116.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.74
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 20-4912913-C-T is Benign according to our data. Variant chr20-4912913-C-T is described in ClinVar as [Benign]. Clinvar id is 791483.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.74 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0117 (1738/148230) while in subpopulation AFR AF= 0.0405 (1632/40316). AF 95% confidence interval is 0.0388. There are 37 homozygotes in gnomad4. There are 828 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 1737 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC23A2NM_005116.6 linkuse as main transcriptc.174G>A p.Ala58= synonymous_variant 4/17 ENST00000338244.6
SLC23A2NM_203327.2 linkuse as main transcriptc.174G>A p.Ala58= synonymous_variant 4/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC23A2ENST00000338244.6 linkuse as main transcriptc.174G>A p.Ala58= synonymous_variant 4/171 NM_005116.6 P1Q9UGH3-1
SLC23A2ENST00000379333.5 linkuse as main transcriptc.174G>A p.Ala58= synonymous_variant 4/171 P1Q9UGH3-1
SLC23A2ENST00000468355.5 linkuse as main transcriptn.540G>A non_coding_transcript_exon_variant 4/121

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0117
AC:
1737
AN:
148108
Hom.:
37
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0406
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00459
Gnomad ASJ
AF:
0.00353
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00345
Gnomad NFE
AF:
0.000121
Gnomad OTH
AF:
0.00846
GnomAD3 exomes
AF:
0.00339
AC:
848
AN:
249964
Hom.:
10
AF XY:
0.00252
AC XY:
341
AN XY:
135110
show subpopulations
Gnomad AFR exome
AF:
0.0434
Gnomad AMR exome
AF:
0.00175
Gnomad ASJ exome
AF:
0.00568
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000168
Gnomad OTH exome
AF:
0.00115
GnomAD4 exome
AF:
0.00135
AC:
1972
AN:
1458978
Hom.:
31
Cov.:
30
AF XY:
0.00118
AC XY:
857
AN XY:
725884
show subpopulations
Gnomad4 AFR exome
AF:
0.0442
Gnomad4 AMR exome
AF:
0.00175
Gnomad4 ASJ exome
AF:
0.00479
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000128
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000104
Gnomad4 OTH exome
AF:
0.00259
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0117
AC:
1738
AN:
148230
Hom.:
37
Cov.:
30
AF XY:
0.0114
AC XY:
828
AN XY:
72572
show subpopulations
Gnomad4 AFR
AF:
0.0405
Gnomad4 AMR
AF:
0.00458
Gnomad4 ASJ
AF:
0.00353
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000121
Gnomad4 OTH
AF:
0.00837
Alfa
AF:
0.00586
Hom.:
6
Bravo
AF:
0.0130
EpiCase
AF:
0.000327
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeAug 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
Cadd
Benign
3.5
Dann
Benign
0.92
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs116317600; hg19: chr20-4893559; API