3-157658106-T-C

Position:

• chr3-157658106-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC66A1L	ENST00000461040.5	n.338+12232T>C		intron_variant, non_coding_transcript_variant		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;