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GeneBe

5-139379730-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_005847.5(SLC23A1):c.873T>C(p.Asp291=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000824 in 1,614,032 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00056 ( 12 hom. )

Consequence

SLC23A1
NM_005847.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.599
Variant links:
Genes affected
SLC23A1 (HGNC:10974): (solute carrier family 23 member 1) 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 transporters. The encoded protein is active in bulk vitamin C transport involving epithelial surfaces. Previously, this gene had an official symbol of SLC23A2. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-139379730-A-G is Benign according to our data. Variant chr5-139379730-A-G is described in ClinVar as [Benign]. Clinvar id is 778216.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=-0.599 with no splicing effect.
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 Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC23A1NM_005847.5 linkuse as main transcriptc.873T>C p.Asp291= synonymous_variant 8/15 ENST00000348729.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC23A1ENST00000348729.8 linkuse as main transcriptc.873T>C p.Asp291= synonymous_variant 8/151 NM_005847.5 P1Q9UHI7-1
SLC23A1ENST00000353963.7 linkuse as main transcriptc.885T>C p.Asp295= synonymous_variant 8/151 Q9UHI7-2
SLC23A1ENST00000504513.1 linkuse as main transcriptc.164+226T>C intron_variant 5
SLC23A1ENST00000506512.1 linkuse as main transcriptn.484T>C non_coding_transcript_exon_variant 1/24

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00335
AC:
509
AN:
152034
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0102
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00393
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000221
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00121
AC:
304
AN:
251388
Hom.:
1
AF XY:
0.00105
AC XY:
143
AN XY:
135870
show subpopulations
Gnomad AFR exome
AF:
0.0110
Gnomad AMR exome
AF:
0.00150
Gnomad ASJ exome
AF:
0.00139
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000431
Gnomad OTH exome
AF:
0.00163
GnomAD4 exome
AF:
0.000561
AC:
820
AN:
1461880
Hom.:
12
Cov.:
33
AF XY:
0.000560
AC XY:
407
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.0132
Gnomad4 AMR exome
AF:
0.00157
Gnomad4 ASJ exome
AF:
0.00103
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000140
Gnomad4 OTH exome
AF:
0.00159
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00335
AC:
510
AN:
152152
Hom.:
4
Cov.:
32
AF XY:
0.00319
AC XY:
237
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.0102
Gnomad4 AMR
AF:
0.00393
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00215
Hom.:
0
Bravo
AF:
0.00386
Asia WGS
AF:
0.00144
AC:
5
AN:
3478
EpiCase
AF:
0.000545
EpiControl
AF:
0.000711

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 testingInvitaeJun 19, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
1.5
Dann
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs116375935; hg19: chr5-138715419; API