XM_047418866.1:c.-964+60244A>G

Variant names:

• chr6-63505258-T-C
• rs2984458
• XM_047418866.1:c.-964+60244A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047418866.1(LGSN):​c.-964+60244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 150,674 control chromosomes in the GnomAD database, including 23,312 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 (23312 hom., cov: 27)
• Consequence: LGSN XM_047418866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701584.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289911	ENST00000701584.1		n.133+60840A>G		intron	N/A
	ENSG00000289911	ENST00000825503.1		n.130+60840A>G		intron	N/A
	ENSG00000289911	ENST00000825504.1		n.145+60244A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80355 AN: 150556 Hom.: 23255 Cov.: 27

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.534 AC: 80480 AN: 150674 Hom.: 23312 Cov.: 27 AF XY: 0.530 AC XY: 38955 AN XY: 73510

African (AFR) AF: 0.770 AC: 31491 AN: 40906

American (AMR) AF: 0.534 AC: 8055 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1243 AN: 3464

East Asian (EAS) AF: 0.447 AC: 2276 AN: 5096

South Asian (SAS) AF: 0.491 AC: 2354 AN: 4792

European-Finnish (FIN) AF: 0.376 AC: 3849 AN: 10240

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29551 AN: 67784

Other (OTH) AF: 0.493 AC: 1033 AN: 2096

Alfa AF: 0.480 Hom.: 29978

Bravo AF: 0.557

Asia WGS AF: 0.455 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.46
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs2984458; hg19: chr6-64215163;