1-48228927-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2

The NM_001011547.3(SLC5A9):​c.312C>G​(p.Gly104Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,613,442 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: š‘“ 0.00094 ( 0 hom., cov: 32)
Exomes š‘“: 0.0017 ( 2 hom. )

Consequence

SLC5A9
NM_001011547.3 synonymous

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.188
Variant links:
Genes affected
SLC5A9 (HGNC:22146): (solute carrier family 5 member 9) Predicted to enable glucose:sodium symporter activity. Predicted to be involved in sodium ion transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 1-48228927-C-G is Benign according to our data. Variant chr1-48228927-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3047851.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.188 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC5A9NM_001011547.3 linkc.312C>G p.Gly104Gly synonymous_variant Exon 3 of 14 ENST00000438567.7 NP_001011547.2 Q2M3M2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC5A9ENST00000438567.7 linkc.312C>G p.Gly104Gly synonymous_variant Exon 3 of 14 1 NM_001011547.3 ENSP00000401730.2 Q2M3M2-1

Frequencies

GnomAD3 genomes
AF:
0.000940
AC:
143
AN:
152176
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00103
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00168
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000979
AC:
245
AN:
250328
Hom.:
0
AF XY:
0.000998
AC XY:
135
AN XY:
135292
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.000607
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000457
Gnomad FIN exome
AF:
0.0000481
Gnomad NFE exome
AF:
0.00170
Gnomad OTH exome
AF:
0.00131
GnomAD4 exome
AF:
0.00168
AC:
2454
AN:
1461148
Hom.:
2
Cov.:
31
AF XY:
0.00163
AC XY:
1188
AN XY:
726856
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
Gnomad4 AMR exome
AF:
0.000581
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000603
Gnomad4 FIN exome
AF:
0.000152
Gnomad4 NFE exome
AF:
0.00204
Gnomad4 OTH exome
AF:
0.00147
GnomAD4 genome
AF:
0.000939
AC:
143
AN:
152294
Hom.:
0
Cov.:
32
AF XY:
0.000913
AC XY:
68
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.000313
Gnomad4 AMR
AF:
0.000392
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00103
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.00168
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.00102
Hom.:
0
Bravo
AF:
0.000884
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00256
EpiControl
AF:
0.00178

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

SLC5A9-related disorder Benign:1
Jan 05, 2024
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.34
CADD
Benign
14
DANN
Benign
0.69
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
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: rs200586919; hg19: chr1-48694599; API