Variant 2-127639232-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001161403.3(LIMS2):c.*49T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 1,597,422 control chromosomes in the GnomAD database, including 222,430 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 27482 hom., cov: 32)

Exomes 𝑓: 0.51 ( 194948 hom. )

Consequence

LIMS2
NM_001161403.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.500

Variant links:

Genes affected

LIMS2 (HGNC:16084): (LIM zinc finger domain containing 2) This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

LIMS2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 2-127639232-A-G is Benign according to our data. Variant chr2-127639232-A-G is described in ClinVar as [Benign]. Clinvar id is 1257147.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIMS2	NM_001161403.3 linkuse as main transcript	c.*49T>C		3_prime_UTR_variant	10/10	ENST00000355119.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIMS2	ENST00000355119.9 linkuse as main transcript	c.*49T>C		3_prime_UTR_variant	10/10	1	NM_001161403.3	P1	Q7Z4I7-1

Frequencies

GnomAD3 genomes

AF:

0.584

AC:

88569

AN:

151788

Hom.:

27457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.788

Gnomad AMI

AF:

0.527

Gnomad AMR

AF:

0.469

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.689

Gnomad FIN

AF:

0.567

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.510

Gnomad OTH

AF:

0.568

GnomAD3 exomes

AF:

0.521

AC:

125860

AN:

241786

Hom.:

35084

AF XY:

0.532

AC XY:

69468

AN XY:

130622

show subpopulations

Gnomad AFR exome

AF:

0.797

Gnomad AMR exome

AF:

0.359

Gnomad ASJ exome

AF:

0.510

Gnomad EAS exome

AF:

0.262

Gnomad SAS exome

AF:

0.692

Gnomad FIN exome

AF:

0.570

Gnomad NFE exome

AF:

0.518

Gnomad OTH exome

AF:

0.520

GnomAD4 exome

AF:

0.512

AC:

740287

AN:

1445516

Hom.:

194948

Cov.:

AF XY:

0.518

AC XY:

371632

AN XY:

718068

show subpopulations

Gnomad4 AFR exome

AF:

0.801

Gnomad4 AMR exome

AF:

0.376

Gnomad4 ASJ exome

AF:

0.505

Gnomad4 EAS exome

AF:

0.271

Gnomad4 SAS exome

AF:

0.685

Gnomad4 FIN exome

AF:

0.566

Gnomad4 NFE exome

AF:

0.501

Gnomad4 OTH exome

AF:

0.522

GnomAD4 genome

AF:

0.583

AC:

88630

AN:

151906

Hom.:

27482

Cov.:

AF XY:

0.583

AC XY:

43291

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.787

Gnomad4 AMR

AF:

0.468

Gnomad4 ASJ

AF:

0.504

Gnomad4 EAS

AF:

0.257

Gnomad4 SAS

AF:

0.686

Gnomad4 FIN

AF:

0.567

Gnomad4 NFE

AF:

0.510

Gnomad4 OTH

AF:

0.571

Alfa

AF:

0.524

Hom.:

9651

Bravo

AF:

0.578

Asia WGS

AF:

0.524

AC:

1824

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 06, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.55

DANN

Benign

0.28

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over