rs367611972
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_022082.4(SLC17A9):c.186C>A(p.Ala62Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A62A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
SLC17A9
NM_022082.4 synonymous
NM_022082.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.55
Publications
0 publications found
Genes affected
SLC17A9 (HGNC:16192): (solute carrier family 17 member 9) This gene encodes a member of a family of transmembrane proteins that are involved in the transport of small molecules. The encoded protein participates in the vesicular uptake, storage, and secretion of adenoside triphosphate (ATP) and other nucleotides. A mutation in this gene was found in individuals with autosomal dominant disseminated superficial actinic porokeratosis-8. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
SLC17A9 Gene-Disease associations (from GenCC):
- disseminated superficial actinic porokeratosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- porokeratosis 8, disseminated superficial actinic typeInheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP7
Synonymous conserved (PhyloP=-3.55 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLC17A9 | NM_022082.4 | c.186C>A | p.Ala62Ala | synonymous_variant | Exon 2 of 13 | ENST00000370351.9 | NP_071365.4 | |
| SLC17A9 | NM_001302643.2 | c.168C>A | p.Ala56Ala | synonymous_variant | Exon 3 of 14 | NP_001289572.2 | ||
| SLC17A9 | XR_936601.4 | n.308C>A | non_coding_transcript_exon_variant | Exon 2 of 10 | ||||
| SLC17A9 | XM_011528978.3 | c.-149C>A | 5_prime_UTR_variant | Exon 1 of 12 | XP_011527280.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC17A9 | ENST00000370351.9 | c.186C>A | p.Ala62Ala | synonymous_variant | Exon 2 of 13 | 1 | NM_022082.4 | ENSP00000359376.4 | ||
| SLC17A9 | ENST00000370349.7 | c.168C>A | p.Ala56Ala | synonymous_variant | Exon 3 of 14 | 1 | ENSP00000359374.3 | |||
| SLC17A9 | ENST00000411611.1 | c.246C>A | p.Ala82Ala | synonymous_variant | Exon 2 of 3 | 2 | ENSP00000388215.1 | |||
| SLC17A9 | ENST00000488738.5 | n.306C>A | non_coding_transcript_exon_variant | Exon 2 of 11 | 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461288Hom.: 0 Cov.: 78 AF XY: 0.00 AC XY: 0AN XY: 726964 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461288
Hom.:
Cov.:
78
AF XY:
AC XY:
0
AN XY:
726964
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44718
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
52852
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111996
Other (OTH)
AF:
AC:
0
AN:
60386
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
34
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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