rs1353890

Positions:

• chr3-157642608-T-C

Variant summary

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

The ENST00000461040.5(SLC66A1L):​n.232-3160T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 152,272 control chromosomes in the GnomAD database, including 252 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 0.038 (252 hom., cov: 32)
• Consequence: SLC66A1L ENST00000461040.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC66A1L	ENST00000461040.5	n.232-3160T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0375 AC: 5704 AN: 152154 Hom.: 247 Cov.: 32

Gnomad AFR AF: 0.00702

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0376 AC: 5719 AN: 152272 Hom.: 252 Cov.: 32 AF XY: 0.0411 AC XY: 3062 AN XY: 74438

Gnomad4 AFR AF: 0.00700

Gnomad4 AMR AF: 0.0967

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.0292

Gnomad4 OTH AF: 0.0359

Alfa AF: 0.0347 Hom.: 22

Bravo AF: 0.0400

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.22
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353890; hg19: chr3-157360397;