ENST00000504880.5:n.115-19606A>G

Variant names:

• chr5-55732332-T-C
• rs3846513
• ENST00000504880.5:n.115-19606A>G

Variant summary

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

The ENST00000504880.5(SLC38A9):​n.115-19606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 152,280 control chromosomes in the GnomAD database, including 71,499 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 0.97 (71499 hom., cov: 31)
• Consequence: SLC38A9 ENST00000504880.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 2 publications found

Genes affected

SLC38A9 (HGNC:26907): (solute carrier family 38 member 9) Enables L-arginine transmembrane transporter activity and L-leucine transmembrane transporter activity. Involved in amino acid transmembrane transport; cellular response to amino acid stimulus; and positive regulation of TOR signaling. Located in late endosome and lysosomal membrane. Is integral component of lysosomal membrane. Colocalizes with Ragulator complex. [provided by Alliance of Genome Resources, Apr 2022]

SLC38A9 Gene-Disease associations (from GenCC):

• lysosomal storage disease

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504880.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A9	ENST00000504880.5	TSL:5	n.115-19606A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147403 AN: 152162 Hom.: 71440 Cov.: 31

Gnomad AFR AF: 0.992

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.969 AC: 147521 AN: 152280 Hom.: 71499 Cov.: 31 AF XY: 0.968 AC XY: 72051 AN XY: 74450

African (AFR) AF: 0.992 AC: 41235 AN: 41570

American (AMR) AF: 0.968 AC: 14800 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3360 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5190 AN: 5190

South Asian (SAS) AF: 0.996 AC: 4794 AN: 4814

European-Finnish (FIN) AF: 0.923 AC: 9781 AN: 10596

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65189 AN: 68032

Other (OTH) AF: 0.961 AC: 2027 AN: 2110

Alfa AF: 0.963 Hom.: 115427

Bravo AF: 0.973

Asia WGS AF: 0.997 AC: 3467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.84
PhyloP100		0.0080

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3846513; hg19: chr5-55028160;