rs792747

Variant names:

• chr3-157658106-T-C
• rs792747
• ENST00000461040.5:n.338+12232T>C

Variant summary

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

The ENST00000461040.5(SLC66A1L):​n.338+12232T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,022 control chromosomes in the GnomAD database, including 10,951 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 0.37 (10951 hom., cov: 32)
• Consequence: SLC66A1L ENST00000461040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 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.338+12232T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56022 AN: 151904 Hom.: 10941 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.369 AC: 56073 AN: 152022 Hom.: 10951 Cov.: 32 AF XY: 0.365 AC XY: 27122 AN XY: 74316

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.376

Alfa AF: 0.328 Hom.: 4685

Bravo AF: 0.374

Asia WGS AF: 0.287 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs792747; hg19: chr3-157375895;