Genetic Variant EEF1B2P5:n.408C>T (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

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

EEF1B2P5 links:

ENSG00000289911 (HGNC:):

ENSG00000289911 links:

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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1B2P5		n.63480541C>T		intragenic_variant
LGSN	XM_047418866.1 link	c.-963-36783G>A		intron_variant	Intron 1 of 11		XP_047274822.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EEF1B2P5	ENST00000444820.2 link	n.408C>T	non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000289911	ENST00000701584.1 link	n.134-36783G>A	intron_variant	Intron 1 of 5
ENSG00000289911	ENST00000825503.1 link	n.131-36783G>A	intron_variant	Intron 1 of 3

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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over