rs9849733

Variant names:

• chr3-157676472-T-C
• rs9849733
• ENST00000461040.5:n.339-1053T>C

Variant summary

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

The ENST00000461040.5(SLC66A1L):​n.339-1053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,092 control chromosomes in the GnomAD database, including 17,089 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 0.38 (17089 hom., cov: 32)
• Consequence: SLC66A1L ENST00000461040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 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.339-1053T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58332 AN: 151972 Hom.: 17033 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.384 AC: 58447 AN: 152092 Hom.: 17089 Cov.: 32 AF XY: 0.379 AC XY: 28191 AN XY: 74348

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.363

Alfa AF: 0.280 Hom.: 1521

Bravo AF: 0.406

Asia WGS AF: 0.291 AC: 1009 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9849733; hg19: chr3-157394261;