rs16884434

Positions:

• chr5-55683170-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173514.4(SLC38A9):​c.114-10475T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,040 control chromosomes in the GnomAD database, including 27,948 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 0.60 (27948 hom., cov: 31)
• Consequence: SLC38A9 NM_173514.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC38A9	NM_173514.4	c.114-10475T>C		intron_variant		ENST00000396865.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC38A9	ENST00000396865.7	c.114-10475T>C		intron_variant		1	NM_173514.4	P1

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91151 AN: 151922 Hom.: 27939 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.600 AC: 91203 AN: 152040 Hom.: 27948 Cov.: 31 AF XY: 0.602 AC XY: 44714 AN XY: 74310

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.609

Alfa AF: 0.633 Hom.: 5219

Bravo AF: 0.582

Asia WGS AF: 0.591 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs16884434; hg19: chr5-54978998;