rs367611972

Variant summary

Our verdict is Likely benign. Variant got -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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.55
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -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
SLC17A9NM_022082.4 linkc.186C>A p.Ala62Ala synonymous_variant Exon 2 of 13 ENST00000370351.9 NP_071365.4 Q9BYT1-1
SLC17A9NM_001302643.2 linkc.168C>A p.Ala56Ala synonymous_variant Exon 3 of 14 NP_001289572.2 Q9BYT1-2H0UI90
SLC17A9XM_011528978.3 linkc.-149C>A 5_prime_UTR_variant Exon 1 of 12 XP_011527280.1
SLC17A9XR_936601.4 linkn.308C>A non_coding_transcript_exon_variant Exon 2 of 10

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC17A9ENST00000370351.9 linkc.186C>A p.Ala62Ala synonymous_variant Exon 2 of 13 1 NM_022082.4 ENSP00000359376.4 Q9BYT1-1
SLC17A9ENST00000370349.7 linkc.168C>A p.Ala56Ala synonymous_variant Exon 3 of 14 1 ENSP00000359374.3 Q9BYT1-2
SLC17A9ENST00000411611.1 linkc.246C>A p.Ala82Ala synonymous_variant Exon 2 of 3 2 ENSP00000388215.1 Q5W197
SLC17A9ENST00000488738.5 linkn.306C>A non_coding_transcript_exon_variant Exon 2 of 11 2

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461288
Hom.:
0
Cov.:
78
AF XY:
0.00
AC XY:
0
AN XY:
726964
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
0.31
DANN
Benign
0.68
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-61588243; API