Genetic Variant LGSN:c.-963-36783G>A (chr6-63480541-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000444820.2(EEF1B2P5):n.408C>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 0.465 in 152,346 control chromosomes in the GnomAD database, including 18,329 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 0.46 ( 18148 hom., cov: 30)

Exomes 𝑓: 0.66 ( 181 hom. )

Consequence

EEF1B2P5
ENST00000444820.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.81

Publications

3 publications found

Variant links:

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]

LGSN links:

EEF1B2P5 (HGNC:32476): (eukaryotic translation elongation factor 1 beta 2 pseudogene 5)

EEF1B2P5 links:

ENSG00000289911 (HGNC:):

ENSG00000289911 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000444820.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444820.2. 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
EEF1B2P5	ENST00000444820.2	TSL:6	n.408C>T	non_coding_transcript_exon	Exon 1 of 2
ENSG00000289911	ENST00000701584.1		n.134-36783G>A	intron	N/A
ENSG00000289911	ENST00000825503.1		n.131-36783G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70363

AN:

151444

Hom.:

18157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.636

Gnomad EAS

AF:

0.550

Gnomad SAS

AF:

0.515

Gnomad FIN

AF:

0.619

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.564

Gnomad OTH

AF:

0.508

GnomAD4 exome

AF:

0.659

AC:

522

AN:

792

Hom.:

181

Cov.:

AF XY:

0.673

AC XY:

268

AN XY:

398

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.669

AC:

475

AN:

710

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.621

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.464

AC:

70354

AN:

151554

Hom.:

18148

Cov.:

AF XY:

0.468

AC XY:

34656

AN XY:

74044

show subpopulations

African (AFR)

AF:

0.228

AC:

9399

AN:

41278

American (AMR)

AF:

0.464

AC:

7068

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.636

AC:

2207

AN:

3468

East Asian (EAS)

AF:

0.550

AC:

2823

AN:

5134

South Asian (SAS)

AF:

0.514

AC:

2472

AN:

4808

European-Finnish (FIN)

AF:

0.619

AC:

6457

AN:

10432

Middle Eastern (MID)

AF:

0.541

AC:

157

AN:

290

European-Non Finnish (NFE)

AF:

0.564

AC:

38292

AN:

67908

Other (OTH)

AF:

0.507

AC:

1066

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

1757

3513

5270

7026

8783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.533

Hom.:

11078

Bravo

AF:

0.442

Asia WGS

AF:

0.547

AC:

1903

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

1.7

(source)

DANN

Benign

0.67

PhyloP100

1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over