NM_022082.4:c.398-807C>T

Variant names:

• chr20-62959697-C-T
• rs2427462
• NM_022082.4:c.398-807C>T

Variant summary

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

The NM_022082.4(SLC17A9):​c.398-807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,146 control chromosomes in the GnomAD database, including 15,832 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 0.43 (15832 hom., cov: 34)
• Consequence: SLC17A9 NM_022082.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.33
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A9	NM_022082.4	c.398-807C>T		intron_variant	Intron 3 of 12	ENST00000370351.9	NP_071365.4
SLC17A9	NM_001302643.2	c.380-807C>T		intron_variant	Intron 4 of 13		NP_001289572.2
SLC17A9	XM_011528978.3	c.38-807C>T		intron_variant	Intron 2 of 11		XP_011527280.1
SLC17A9	XR_936601.4	n.520-807C>T		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A9	ENST00000370351.9	c.398-807C>T		intron_variant	Intron 3 of 12	1	NM_022082.4	ENSP00000359376.4
SLC17A9	ENST00000370349.7	c.380-807C>T		intron_variant	Intron 4 of 13	1		ENSP00000359374.3
SLC17A9	ENST00000488738.5	n.518-807C>T		intron_variant	Intron 3 of 10	2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65486 AN: 152028 Hom.: 15836 Cov.: 34

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.430 AC: 65483 AN: 152146 Hom.: 15832 Cov.: 34 AF XY: 0.443 AC XY: 32919 AN XY: 74366

African (AFR) AF: 0.201 AC: 8326 AN: 41524

American (AMR) AF: 0.512 AC: 7831 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1740 AN: 3472

East Asian (EAS) AF: 0.754 AC: 3885 AN: 5154

South Asian (SAS) AF: 0.626 AC: 3024 AN: 4828

European-Finnish (FIN) AF: 0.590 AC: 6245 AN: 10584

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32935 AN: 67978

Other (OTH) AF: 0.456 AC: 962 AN: 2110

Alfa AF: 0.466 Hom.: 20458

Bravo AF: 0.414

Asia WGS AF: 0.664 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.59
PhyloP100		-4.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2427462; hg19: chr20-61591049; COSMIC: COSV64847961; COSMIC: COSV64847961;