rs1630182

Positions:

• chr6-63498307-G-A

Variant summary

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

The XM_047418866.1(LGSN):​c.-963-54549C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,794 control chromosomes in the GnomAD database, including 23,566 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 0.53 (23566 hom., cov: 32)
• Consequence: LGSN XM_047418866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906

Genes affected

LGSN (HGNC:21016): (lengsin, lens protein with glutamine synthetase domain) This gene encodes a protein with similarity to the GS I members of the glutamine synthetase superfamily. The encoded protein is referred to as a pseudo-glutamine synthetase because it has no glutamine synthesis activity and may function as a chaperone protein. This protein is localized to the lens and may be associated with cataract disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]

ENSG00000289911 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGSN	XM_047418866.1	c.-963-54549C>T		intron_variant			XP_047274822.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289911	ENST00000701584.1	n.134-54549C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81053 AN: 151676 Hom.: 23508 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.535 AC: 81180 AN: 151794 Hom.: 23566 Cov.: 32 AF XY: 0.531 AC XY: 39384 AN XY: 74176

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.492

Alfa AF: 0.480 Hom.: 3058

Bravo AF: 0.556

Asia WGS AF: 0.455 AC: 1580 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	8.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1630182; hg19: chr6-64208212;