rs11958779

Positions:

• chr5-55706071-G-A

Variant summary

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

The NM_173514.4(SLC38A9):​c.-35+5381C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,610 control chromosomes in the GnomAD database, including 30,769 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 0.63 (30769 hom., cov: 31)
• Consequence: SLC38A9 NM_173514.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC38A9	NM_173514.4	c.-35+5381C>T		intron_variant		ENST00000396865.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC38A9	ENST00000396865.7	c.-35+5381C>T		intron_variant		1	NM_173514.4	P1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 95902 AN: 151492 Hom.: 30771 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.633 AC: 95938 AN: 151610 Hom.: 30769 Cov.: 31 AF XY: 0.634 AC XY: 46937 AN XY: 74050

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.640

Alfa AF: 0.671 Hom.: 25125

Bravo AF: 0.617

Asia WGS AF: 0.608 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.66

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: rs11958779; hg19: chr5-55001899;