Genetic Variant SLC17A9:p.Leu110Leu (chr20-62957513-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_022082.4(SLC17A9):c.330C>T(p.Leu110Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 1,610,046 control chromosomes in the GnomAD database, including 3,380 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.050 ( 268 hom., cov: 33)

Exomes 𝑓: 0.062 ( 3112 hom. )

Consequence

SLC17A9
NM_022082.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.495

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 20-62957513-C-T is Benign according to our data. Variant chr20-62957513-C-T is described in ClinVar as [Benign]. Clinvar id is 3056817.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.495 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A9	NM_022082.4 link	c.330C>T	p.Leu110Leu	synonymous_variant	Exon 3 of 13	ENST00000370351.9	NP_071365.4	Q9BYT1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC17A9	ENST00000370351.9 link	c.330C>T	p.Leu110Leu	synonymous_variant	Exon 3 of 13	1	NM_022082.4	ENSP00000359376.4	Q9BYT1-1
SLC17A9	ENST00000370349.7 link	c.312C>T	p.Leu104Leu	synonymous_variant	Exon 4 of 14	1		ENSP00000359374.3	Q9BYT1-2
SLC17A9	ENST00000411611.1 link	c.390C>T	p.Leu130Leu	synonymous_variant	Exon 3 of 3	2		ENSP00000388215.1	Q5W197
SLC17A9	ENST00000488738.5 link	n.450C>T		non_coding_transcript_exon_variant	Exon 3 of 11	2

Frequencies

GnomAD3 genomes

AF:

0.0500

AC:

7605

AN:

152148

Hom.:

268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0129

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0391

Gnomad ASJ

AF:

0.0438

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0310

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0707

Gnomad OTH

AF:

0.0458

GnomAD3 exomes

AF:

0.0519

AC:

12707

AN:

244648

Hom.:

480

AF XY:

0.0529

AC XY:

7041

AN XY:

133090

show subpopulations

Gnomad AFR exome

AF:

0.0109

Gnomad AMR exome

AF:

0.0230

Gnomad ASJ exome

AF:

0.0470

Gnomad EAS exome

AF:

0.000571

Gnomad SAS exome

AF:

0.0287

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.0715

Gnomad OTH exome

AF:

0.0556

GnomAD4 exome

AF:

0.0624

AC:

90936

AN:

1457780

Hom.:

3112

Cov.:

AF XY:

0.0612

AC XY:

44415

AN XY:

725264

show subpopulations

Gnomad4 AFR exome

AF:

0.0101

Gnomad4 AMR exome

AF:

0.0248

Gnomad4 ASJ exome

AF:

0.0458

Gnomad4 EAS exome

AF:

0.000483

Gnomad4 SAS exome

AF:

0.0313

Gnomad4 FIN exome

AF:

0.0975

Gnomad4 NFE exome

AF:

0.0694

Gnomad4 OTH exome

AF:

0.0546

GnomAD4 genome

AF:

0.0499

AC:

7605

AN:

152266

Hom.:

268

Cov.:

AF XY:

0.0508

AC XY:

3782

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0129

Gnomad4 AMR

AF:

0.0391

Gnomad4 ASJ

AF:

0.0438

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0317

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.0707

Gnomad4 OTH

AF:

0.0454

Alfa

AF:

0.0589

Hom.:

148

Bravo

AF:

0.0428

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC17A9-related disorder

Benign:1

Apr 15, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as 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

-0.72

CADD

Benign

0.28

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over