20-62959988-G-C

Variant names:

• chr20-62959988-G-C
• rs910933
• NM_022082.4:c.398-516G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022082.4(SLC17A9):​c.398-516G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,274 control chromosomes in the GnomAD database, including 39,395 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (39395 hom., cov: 35)
• Consequence: SLC17A9 NM_022082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 2 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 porokeratosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• porokeratosis 8, disseminated superficial actinic type

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022082.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A9	NM_022082.4	MANE Select	c.398-516G>C		intron	N/A	NP_071365.4
	SLC17A9	NM_001302643.2		c.380-516G>C		intron	N/A	NP_001289572.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A9	ENST00000370351.9	TSL:1 MANE Select	c.398-516G>C		intron	N/A	ENSP00000359376.4
	SLC17A9	ENST00000370349.7	TSL:1	c.380-516G>C		intron	N/A	ENSP00000359374.3
	SLC17A9	ENST00000488738.5	TSL:2	n.518-516G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.684 AC: 104014 AN: 152156 Hom.: 39390 Cov.: 35

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.724

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.683 AC: 104029 AN: 152274 Hom.: 39395 Cov.: 35 AF XY: 0.692 AC XY: 51544 AN XY: 74456

African (AFR) AF: 0.326 AC: 13536 AN: 41546

American (AMR) AF: 0.813 AC: 12452 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2903 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5147 AN: 5176

South Asian (SAS) AF: 0.823 AC: 3974 AN: 4828

European-Finnish (FIN) AF: 0.820 AC: 8699 AN: 10614

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54858 AN: 68010

Other (OTH) AF: 0.725 AC: 1535 AN: 2116

Alfa AF: 0.738 Hom.: 5457

Bravo AF: 0.667

Asia WGS AF: 0.873 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.58
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs910933; hg19: chr20-61591340;