ENST00000825519.1:n.1259C>T

Variant names:

• chr6-63374900-G-A
• rs2677024
• ENST00000825519.1:n.1259C>T

Variant summary

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

The ENST00000825519.1(ENSG00000289911):​n.1259C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,970 control chromosomes in the GnomAD database, including 2,454 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 (2454 hom., cov: 32)
• Consequence: ENSG00000289911 ENST00000825519.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 1 publications found

Genes affected

ENSG00000289911 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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: ENST00000825519.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289911	ENST00000825519.1		n.1259C>T		non_coding_transcript_exon	Exon 7 of 7
	ENSG00000289911	ENST00000825503.1		n.306-24059C>T		intron	N/A
	ENSG00000289911	ENST00000825504.1		n.683+4396C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18380 AN: 151852 Hom.: 2440 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.0722

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.121 AC: 18438 AN: 151970 Hom.: 2454 Cov.: 32 AF XY: 0.118 AC XY: 8777 AN XY: 74292

African (AFR) AF: 0.335 AC: 13860 AN: 41386

American (AMR) AF: 0.0690 AC: 1054 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0279 AC: 97 AN: 3472

East Asian (EAS) AF: 0.0972 AC: 503 AN: 5174

South Asian (SAS) AF: 0.0714 AC: 344 AN: 4818

European-Finnish (FIN) AF: 0.0215 AC: 227 AN: 10544

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0299 AC: 2035 AN: 67988

Other (OTH) AF: 0.0972 AC: 205 AN: 2108

Alfa AF: 0.0539 Hom.: 1081

Bravo AF: 0.134

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.55
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs2677024; hg19: chr6-64084805;