Variant chr2-105361304-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001318895.3(FHL2):c.819C>T(p.Pro273=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 1,613,040 control chromosomes in the GnomAD database, including 27,859 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2145 hom., cov: 32)

Exomes 𝑓: 0.18 ( 25714 hom. )

Consequence

FHL2
NM_001318895.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -4.19

Variant links:

Genes affected

FHL2 (HGNC:3703): (four and a half LIM domains 2) This gene encodes a member of the four-and-a-half-LIM-only protein family. Family members contain two highly conserved, tandemly arranged, zinc finger domains with four highly conserved cysteines binding a zinc atom in each zinc finger. This protein is thought to have a role in the assembly of extracellular membranes. Also, this gene is down-regulated during transformation of normal myoblasts to rhabdomyosarcoma cells and the encoded protein may function as a link between presenilin-2 and an intracellular signaling pathway. Multiple alternatively spliced variants encoding different isoforms have been identified. [provided by RefSeq, Jan 2016]

FHL2 links:

C2orf49 (HGNC:):

C2orf49 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 2-105361304-G-A is Benign according to our data. Variant chr2-105361304-G-A is described in ClinVar as [Benign]. Clinvar id is 48332.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-105361304-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-4.19 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FHL2	NM_001318895.3 linkuse as main transcript	c.819C>T	p.Pro273=	synonymous_variant	7/7	ENST00000530340.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FHL2	ENST00000530340.6 linkuse as main transcript	c.819C>T	p.Pro273=	synonymous_variant	7/7	1	NM_001318895.3	P1	Q14192-1

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24171

AN:

152098

Hom.:

2147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.0250

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.158

AC:

39675

AN:

250382

Hom.:

3639

AF XY:

0.162

AC XY:

21900

AN XY:

135300

show subpopulations

Gnomad AFR exome

AF:

0.0995

Gnomad AMR exome

AF:

0.0914

Gnomad ASJ exome

AF:

0.216

Gnomad EAS exome

AF:

0.0253

Gnomad SAS exome

AF:

0.131

Gnomad FIN exome

AF:

0.247

Gnomad NFE exome

AF:

0.193

Gnomad OTH exome

AF:

0.179

GnomAD4 exome

AF:

0.182

AC:

266232

AN:

1460824

Hom.:

25714

Cov.:

AF XY:

0.182

AC XY:

132086

AN XY:

726712

show subpopulations

Gnomad4 AFR exome

AF:

0.0978

Gnomad4 AMR exome

AF:

0.0962

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.0213

Gnomad4 SAS exome

AF:

0.129

Gnomad4 FIN exome

AF:

0.243

Gnomad4 NFE exome

AF:

0.195

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.159

AC:

24170

AN:

152216

Hom.:

2145

Cov.:

AF XY:

0.160

AC XY:

11901

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.139

Gnomad4 ASJ

AF:

0.216

Gnomad4 EAS

AF:

0.0253

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.251

Gnomad4 NFE

AF:

0.192

Gnomad4 OTH

AF:

0.165

Alfa

AF:

0.182

Hom.:

1399

Bravo

AF:

0.149

Asia WGS

AF:

0.0810

AC:

282

AN:

3478

EpiCase

AF:

0.202

EpiControl

AF:

0.200

ClinVar

Significance: Benign

Submissions summary: Benign:4

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	Sep 06, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Sep 16, 2011

This variant is classified as benign because it does not change the amino acid a nd is frequent in the general population (rs11124029, MAF >1%). -

Primary dilated cardiomyopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.41

DANN

Benign

0.61

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