Genetic Variant SLC17A9:p.Ala13Gly (chr20-62952868-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_022082.4(SLC17A9):c.38C>G(p.Ala13Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000877 in 1,139,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A13D) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 8.8e-7 ( 0 hom. )

Consequence

SLC17A9
NM_022082.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.495

Publications

0 publications found

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]

SLC17A9 Gene-Disease associations (from GenCC):

disseminated superficial actinic porokeratosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
porokeratosis 8, disseminated superficial actinic type
Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

SLC17A9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.12656799).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A9	NM_022082.4 link	c.38C>G	p.Ala13Gly	missense_variant	Exon 1 of 13	ENST00000370351.9	NP_071365.4	Q9BYT1-1
SLC17A9	XR_936601.4 link	n.160C>G		non_coding_transcript_exon_variant	Exon 1 of 10
SLC17A9	NM_001302643.2 link	c.-43C>G		5_prime_UTR_variant	Exon 1 of 14		NP_001289572.2	Q9BYT1-2H0UI90

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC17A9	ENST00000370351.9 link	c.38C>G	p.Ala13Gly	missense_variant	Exon 1 of 13	1	NM_022082.4	ENSP00000359376.4	Q9BYT1-1
SLC17A9	ENST00000370349.7 link	c.-43C>G		5_prime_UTR_variant	Exon 1 of 14	1		ENSP00000359374.3	Q9BYT1-2
SLC17A9	ENST00000488738.5 link	n.158C>G		non_coding_transcript_exon_variant	Exon 1 of 11	2
SLC17A9	ENST00000411611.1 link	c.-286C>G		upstream_gene_variant		2		ENSP00000388215.1	Q5W197

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.77e-7

AC:

AN:

1139952

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

558386

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24440

American (AMR)

AF:

0.00

AC:

AN:

26354

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15526

East Asian (EAS)

AF:

0.00

AC:

AN:

14786

South Asian (SAS)

AF:

0.00

AC:

AN:

74562

European-Finnish (FIN)

AF:

0.00

AC:

AN:

16880

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2784

European-Non Finnish (NFE)

AF:

0.00000108

AC:

AN:

922828

Other (OTH)

AF:

0.00

AC:

AN:

41792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Benign

0.87

DEOGEN2

Benign

0.050

Eigen

Benign

-0.83

Eigen_PC

Benign

-0.84

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.43

M_CAP

Pathogenic

0.49

MetaRNN

Benign

0.13

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.70

PhyloP100

0.49

PrimateAI

Uncertain

0.63

PROVEAN

Benign

-0.83

REVEL

Benign

0.15

Sift

Benign

0.28

Sift4G

Benign

0.39

Polyphen

0.0010

Vest4

0.13

MutPred

0.17

Loss of catalytic residue at A13 (P = 0.0525);

MVP

0.081

MPC

0.43

ClinPred

0.063

GERP RS

3.0

PromoterAI

-0.18

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.070

gMVP

0.14

Mutation Taster

=90/10

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over