20-62952868-C-A

Variant names:

• chr20-62952868-C-A
• rs2065502161
• NM_022082.4:c.38C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_022082.4(SLC17A9):​c.38C>A​(p.Ala13Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000877 in 1,139,952 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 (★).

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 8.8e-7 (0 hom.)
• Consequence: SLC17A9 NM_022082.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.495
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14990023).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A9	NM_022082.4	c.38C>A	p.Ala13Asp	missense_variant	Exon 1 of 13	ENST00000370351.9	NP_071365.4
SLC17A9	XR_936601.4	n.160C>A		non_coding_transcript_exon_variant	Exon 1 of 10
SLC17A9	NM_001302643.2	c.-43C>A		5_prime_UTR_variant	Exon 1 of 14		NP_001289572.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A9	ENST00000370351.9	c.38C>A	p.Ala13Asp	missense_variant	Exon 1 of 13	1	NM_022082.4	ENSP00000359376.4
SLC17A9	ENST00000370349.7	c.-43C>A		5_prime_UTR_variant	Exon 1 of 14	1		ENSP00000359374.3
SLC17A9	ENST00000488738.5	n.158C>A		non_coding_transcript_exon_variant	Exon 1 of 11	2
SLC17A9	ENST00000411611.1	c.-286C>A		upstream_gene_variant		2		ENSP00000388215.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 8.77e-7 AC: 1 AN: 1139952 Hom.: 0 Cov.: 33 AF XY: 0.00000179 AC XY: 1 AN XY: 558386

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 24440

American (AMR) AF: 0.0000379 AC: 1 AN: 26354

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15526

East Asian (EAS) AF: 0.00 AC: 0 AN: 14786

South Asian (SAS) AF: 0.00 AC: 0 AN: 74562

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16880

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2784

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 922828

Other (OTH) AF: 0.00 AC: 0 AN: 41792

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 30

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 06, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.38C>A (p.A13D) alteration is located in exon 1 (coding exon 1) of the SLC17A9 gene. This alteration results from a C to A substitution at nucleotide position 38, causing the alanine (A) at amino acid position 13 to be replaced by an aspartic acid (D). 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	0.096
BayesDel_addAF	Benign	-0.051	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	13
DANN	Benign	0.94
DEOGEN2	Benign	0.024	T
Eigen	Benign	-0.85
Eigen_PC	Benign	-0.86
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.42	T
M_CAP	Pathogenic	0.65	D
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.49
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-0.32	N
REVEL	Benign	0.23
Sift	Benign	0.27	T
Sift4G	Benign	0.53	T
Polyphen		0.013	B
Vest4		0.13
MutPred		0.27		Loss of catalytic residue at A13 (P = 0.014);
MVP		0.11
MPC		0.78
ClinPred		0.11	T
GERP RS		3.0
PromoterAI		0.082	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.10
gMVP		0.33
Mutation Taster		=84/16	polymorphism

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: rs2065502161; hg19: chr20-61584220;