rs1499793

Variant names:

• chr3-157643508-C-T
• rs1499793
• ENST00000461040.5:n.232-2260C>T

Variant summary

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

The ENST00000461040.5(SLC66A1L):​n.232-2260C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,062 control chromosomes in the GnomAD database, including 4,088 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 0.22 (4088 hom., cov: 32)
• Consequence: SLC66A1L ENST00000461040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

SLC66A1L (HGNC:25146): (solute carrier family 66 member 1 like, pseudogene) Predicted to enable L-arginine transmembrane transporter activity and L-lysine transmembrane transporter activity. Predicted to be involved in L-arginine transmembrane transport and L-lysine transmembrane transport. Predicted to be active in lysosomal membrane. Predicted to be integral component of membrane. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC66A1L	ENST00000461040.5	n.232-2260C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32955 AN: 151942 Hom.: 4083 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.217 AC: 32965 AN: 152062 Hom.: 4088 Cov.: 32 AF XY: 0.218 AC XY: 16229 AN XY: 74324

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.246

Alfa AF: 0.238 Hom.: 963

Bravo AF: 0.203

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1499793; hg19: chr3-157361297;