rs1629176

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005116.6(SLC23A2):​c.483-3235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,052 control chromosomes in the GnomAD database, including 12,274 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 0.38 ( 12274 hom., cov: 32)

Consequence

SLC23A2
NM_005116.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC23A2NM_005116.6 linkuse as main transcriptc.483-3235C>T intron_variant ENST00000338244.6
SLC23A2NM_203327.2 linkuse as main transcriptc.483-3235C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC23A2ENST00000338244.6 linkuse as main transcriptc.483-3235C>T intron_variant 1 NM_005116.6 P1Q9UGH3-1
SLC23A2ENST00000379333.5 linkuse as main transcriptc.483-3235C>T intron_variant 1 P1Q9UGH3-1
SLC23A2ENST00000468355.5 linkuse as main transcriptn.849-3235C>T intron_variant, non_coding_transcript_variant 1
SLC23A2ENST00000423430.1 linkuse as main transcriptc.93+10411C>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.383
AC:
58233
AN:
151934
Hom.:
12276
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.217
Gnomad AMI
AF:
0.600
Gnomad AMR
AF:
0.375
Gnomad ASJ
AF:
0.413
Gnomad EAS
AF:
0.243
Gnomad SAS
AF:
0.406
Gnomad FIN
AF:
0.394
Gnomad MID
AF:
0.440
Gnomad NFE
AF:
0.488
Gnomad OTH
AF:
0.395
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.383
AC:
58247
AN:
152052
Hom.:
12274
Cov.:
32
AF XY:
0.378
AC XY:
28084
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.217
Gnomad4 AMR
AF:
0.374
Gnomad4 ASJ
AF:
0.413
Gnomad4 EAS
AF:
0.244
Gnomad4 SAS
AF:
0.407
Gnomad4 FIN
AF:
0.394
Gnomad4 NFE
AF:
0.488
Gnomad4 OTH
AF:
0.391
Alfa
AF:
0.455
Hom.:
8712
Bravo
AF:
0.375
Asia WGS
AF:
0.283
AC:
989
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.36
DANN
Benign
0.86

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: rs1629176; hg19: chr20-4869790; API