rs910933

Positions:

• chr20-62959988-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC17A9	NM_022082.4	c.398-516G>C		intron_variant		ENST00000370351.9	NP_071365.4
SLC17A9	NM_001302643.2	c.380-516G>C		intron_variant			NP_001289572.2
SLC17A9	XM_011528978.3	c.38-516G>C		intron_variant			XP_011527280.1
SLC17A9	XR_936601.4	n.520-516G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC17A9	ENST00000370351.9	c.398-516G>C		intron_variant		1	NM_022082.4	ENSP00000359376	P1
SLC17A9	ENST00000370349.7	c.380-516G>C		intron_variant		1		ENSP00000359374
SLC17A9	ENST00000488738.5	n.518-516G>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.725

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.58

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

Other links and lift over

dbSNP: rs910933; hg19: chr20-61591340;