Variant chr11-33864748-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_005574.4(LMO2):c.318T>C(p.Ile106Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 1,613,586 control chromosomes in the GnomAD database, including 140,981 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.45 ( 15685 hom., cov: 32)

Exomes 𝑓: 0.41 ( 125296 hom. )

Consequence

LMO2
NM_005574.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.261

Variant links:

Genes affected

LMO2 (HGNC:6642): (LIM domain only 2) LMO2 encodes a cysteine-rich, two LIM-domain protein that is required for yolk sac erythropoiesis. The LMO2 protein has a central and crucial role in hematopoietic development and is highly conserved. The LMO2 transcription start site is located approximately 25 kb downstream from the 11p13 T-cell translocation cluster (11p13 ttc), where a number T-cell acute lymphoblastic leukemia-specific translocations occur. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Nov 2008]

LMO2 links:

LMO2 (HGNC:):

LMO2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 11-33864748-A-G is Benign according to our data. Variant chr11-33864748-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.261 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LMO2	NM_005574.4 linkuse as main transcript	c.318T>C	p.Ile106Ile	synonymous_variant	5/6	ENST00000257818.3	NP_005565.2	P25791-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMO2	ENST00000257818.3 linkuse as main transcript	c.318T>C	p.Ile106Ile	synonymous_variant	5/6	1	NM_005574.4	ENSP00000257818.2		P25791-3

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67559

AN:

151872

Hom.:

15635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.551

Gnomad AMI

AF:

0.459

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.323

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.538

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.407

Gnomad OTH

AF:

0.403

GnomAD3 exomes

AF:

0.399

AC:

100039

AN:

250822

Hom.:

21017

AF XY:

0.399

AC XY:

54128

AN XY:

135714

show subpopulations

Gnomad AFR exome

AF:

0.558

Gnomad AMR exome

AF:

0.238

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.387

Gnomad SAS exome

AF:

0.381

Gnomad FIN exome

AF:

0.530

Gnomad NFE exome

AF:

0.414

Gnomad OTH exome

AF:

0.379

GnomAD4 exome

AF:

0.410

AC:

599898

AN:

1461596

Hom.:

125296

Cov.:

AF XY:

0.409

AC XY:

297402

AN XY:

727082

show subpopulations

Gnomad4 AFR exome

AF:

0.558

Gnomad4 AMR exome

AF:

0.246

Gnomad4 ASJ exome

AF:

0.328

Gnomad4 EAS exome

AF:

0.432

Gnomad4 SAS exome

AF:

0.380

Gnomad4 FIN exome

AF:

0.515

Gnomad4 NFE exome

AF:

0.412

Gnomad4 OTH exome

AF:

0.396

GnomAD4 genome

AF:

0.445

AC:

67665

AN:

151990

Hom.:

15685

Cov.:

AF XY:

0.449

AC XY:

33321

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.552

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.323

Gnomad4 EAS

AF:

0.409

Gnomad4 SAS

AF:

0.390

Gnomad4 FIN

AF:

0.538

Gnomad4 NFE

AF:

0.407

Gnomad4 OTH

AF:

0.411

Alfa

AF:

0.406

Hom.:

21106

Bravo

AF:

0.435

Asia WGS

AF:

0.428

AC:

1489

AN:

3478

EpiCase

AF:

0.394

EpiControl

AF:

0.396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

4.8

DANN

Benign

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over