rs1744140

Variant names:

• chr6-63502926-T-C
• rs1744140
• XM_047418866.1:c.-963-59168A>G

Variant summary

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

The ENST00000701584.1(ENSG00000289911):​n.134-59168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,092 control chromosomes in the GnomAD database, including 23,658 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 0.54 (23658 hom., cov: 33)
• Consequence: ENSG00000289911 ENST00000701584.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 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.134-59168A>G		intron	N/A
	ENSG00000289911	ENST00000825503.1		n.131-59168A>G		intron	N/A
	ENSG00000289911	ENST00000825504.1		n.146-59168A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81357 AN: 151974 Hom.: 23600 Cov.: 33

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.544

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: 0.453

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.536 AC: 81483 AN: 152092 Hom.: 23658 Cov.: 33 AF XY: 0.532 AC XY: 39554 AN XY: 74360

African (AFR) AF: 0.771 AC: 32002 AN: 41502

American (AMR) AF: 0.534 AC: 8159 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2331 AN: 5184

South Asian (SAS) AF: 0.494 AC: 2380 AN: 4818

European-Finnish (FIN) AF: 0.383 AC: 4042 AN: 10560

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29652 AN: 67972

Other (OTH) AF: 0.494 AC: 1041 AN: 2106

Alfa AF: 0.484 Hom.: 28352

Bravo AF: 0.557

Asia WGS AF: 0.455 AC: 1578 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1744140; hg19: chr6-64212831;