chr20-62952880-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_022082.4(SLC17A9):c.50A>G(p.Gln17Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 964,538 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. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q17P) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

SLC17A9
NM_022082.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.03

Publications

1 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.049886197).

BS2

High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A9	NM_022082.4 link	c.50A>G	p.Gln17Arg	missense_variant	Exon 1 of 13	ENST00000370351.9	NP_071365.4	Q9BYT1-1
SLC17A9	XR_936601.4 link	n.172A>G		non_coding_transcript_exon_variant	Exon 1 of 10
SLC17A9	NM_001302643.2 link	c.-31A>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.50A>G	p.Gln17Arg	missense_variant	Exon 1 of 13	1	NM_022082.4	ENSP00000359376.4	Q9BYT1-1
SLC17A9	ENST00000370349.7 link	c.-31A>G		5_prime_UTR_variant	Exon 1 of 14	1		ENSP00000359374.3	Q9BYT1-2
SLC17A9	ENST00000488738.5 link	n.170A>G		non_coding_transcript_exon_variant	Exon 1 of 11	2
SLC17A9	ENST00000411611.1 link	c.-274A>G		upstream_gene_variant		2		ENSP00000388215.1	Q5W197

Frequencies

GnomAD3 genomes

AF:

0.000133

AC:

AN:

52576

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000464

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000355

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000295

AC:

AN:

101790

AF XY:

0.0000362

show subpopulations

Gnomad AFR exome

AF:

0.000160

Gnomad AMR exome

AF:

0.000108

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000132

AC:

AN:

911934

Hom.:

Cov.:

AF XY:

0.0000157

AC XY:

AN XY:

446634

show subpopulations

African (AFR)

AF:

0.000299

AC:

AN:

20066

American (AMR)

AF:

0.0000882

AC:

AN:

22678

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12422

East Asian (EAS)

AF:

0.00

AC:

AN:

11756

South Asian (SAS)

AF:

0.00

AC:

AN:

63344

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12372

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2186

European-Non Finnish (NFE)

AF:

0.00000409

AC:

AN:

734232

Other (OTH)

AF:

0.0000304

AC:

AN:

32878

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.000152

AC:

AN:

52604

Hom.:

Cov.:

AF XY:

0.000122

AC XY:

AN XY:

24608

show subpopulations

African (AFR)

AF:

0.000540

AC:

AN:

12958

American (AMR)

AF:

0.00

AC:

AN:

3712

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1488

East Asian (EAS)

AF:

0.00

AC:

AN:

1892

South Asian (SAS)

AF:

0.00

AC:

AN:

1448

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1708

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000355

AC:

AN:

28134

Other (OTH)

AF:

0.00

AC:

AN:

728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.532

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0000843

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Apr 29, 2025

Ambry Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.50A>G (p.Q17R) alteration is located in exon 1 (coding exon 1) of the SLC17A9 gene. This alteration results from a A to G substitution at nucleotide position 50, causing the glutamine (Q) at amino acid position 17 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Benign

-0.63

CADD

Benign

5.2

(source)

DANN

Benign

0.66

DEOGEN2

Benign

0.051

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.053

LIST_S2

Benign

0.35

M_CAP

Uncertain

0.25

MetaRNN

Benign

0.050

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.2

PhyloP100

-1.0

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-0.79

REVEL

Benign

0.022

Sift

Benign

0.41

Sift4G

Benign

0.39

Polyphen

0.0

Vest4

0.078

MutPred

0.31

Loss of catalytic residue at Q17 (P = 0.042);

MVP

0.040

MPC

0.46

ClinPred

0.019

GERP RS

-0.76

PromoterAI

0.0087

Neutral

(source)

Varity_R

0.039

gMVP

0.072

Mutation Taster

=97/3

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

chr20-62952880-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over