XM_017010930.3:c.-288+5741C>T

Variant names:

• chr6-63373555-G-A
• rs2677023
• XM_017010930.3:c.-288+5741C>T

Variant summary

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

The XM_017010930.3(LGSN):​c.-288+5741C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,100 control chromosomes in the GnomAD database, including 2,447 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 0.12 (2447 hom., cov: 32)
• Consequence: LGSN XM_017010930.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825503.1. 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	ENST00000825503.1		n.306-22714C>T		intron	N/A
	ENSG00000289911	ENST00000825504.1		n.683+5741C>T		intron	N/A
	ENSG00000289911	ENST00000825506.1		n.1095+5741C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18369 AN: 151982 Hom.: 2434 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.121 AC: 18425 AN: 152100 Hom.: 2447 Cov.: 32 AF XY: 0.118 AC XY: 8760 AN XY: 74362

African (AFR) AF: 0.334 AC: 13844 AN: 41422

American (AMR) AF: 0.0688 AC: 1052 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3468

East Asian (EAS) AF: 0.0968 AC: 502 AN: 5184

South Asian (SAS) AF: 0.0715 AC: 345 AN: 4826

European-Finnish (FIN) AF: 0.0216 AC: 229 AN: 10590

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0300 AC: 2038 AN: 68004

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.0781 Hom.: 219

Bravo AF: 0.134

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.75
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2677023; hg19: chr6-64083460;