1-37998026-A-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004468.5(FHL3):c.438T>A(p.Gly146Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000397 in 1,614,028 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00021 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00042 ( 6 hom. )
Consequence
FHL3
NM_004468.5 synonymous
NM_004468.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.59
Genes affected
FHL3 (HGNC:3704): (four and a half LIM domains 3) The protein encoded by this gene is a member of a family of proteins containing a four-and-a-half LIM domain, which is a highly conserved double zinc finger motif. The encoded protein has been shown to interact with the cancer developmental regulators SMAD2, SMAD3, and SMAD4, the skeletal muscle myogenesis protein MyoD, and the high-affinity IgE beta chain regulator MZF-1. This protein may be involved in tumor suppression, repression of MyoD expression, and repression of IgE receptor expression. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 1-37998026-A-T is Benign according to our data. Variant chr1-37998026-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638684.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.59 with no splicing effect.
BS2
High AC in GnomAd4 at 32 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FHL3 | ENST00000373016.4 | c.438T>A | p.Gly146Gly | synonymous_variant | Exon 4 of 6 | 1 | NM_004468.5 | ENSP00000362107.3 | ||
FHL3 | ENST00000485803.5 | n.428T>A | non_coding_transcript_exon_variant | Exon 3 of 5 | 1 | |||||
FHL3 | ENST00000477194.5 | n.626T>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 2 | |||||
FHL3 | ENST00000475084.5 | n.322-156T>A | intron_variant | Intron 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152056Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000823 AC: 207AN: 251412Hom.: 2 AF XY: 0.000979 AC XY: 133AN XY: 135898
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GnomAD4 exome AF: 0.000417 AC: 609AN: 1461854Hom.: 6 Cov.: 34 AF XY: 0.000568 AC XY: 413AN XY: 727240
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GnomAD4 genome AF: 0.000210 AC: 32AN: 152174Hom.: 1 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74390
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
FHL3: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at