rs765146615
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000377317.5(FOXH1):āc.864T>Cā(p.Asn288=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 34)
Exomes š: 0.000010 ( 0 hom. )
Consequence
FOXH1
ENST00000377317.5 synonymous
ENST00000377317.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.420
Genes affected
FOXH1 (HGNC:3814): (forkhead box H1) FOXH1 encodes a human homolog of Xenopus forkhead activin signal transducer-1. FOXH1 protein binds SMAD2 and activates an activin response element via binding the DNA motif TGT(G/T)(T/G)ATT. [provided by RefSeq, Jul 2008]
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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=-0.65).
BP6
Variant 8-144474472-A-G is Benign according to our data. Variant chr8-144474472-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 259201.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.42 with no splicing effect.
BS2
High AC in GnomAdExome4 at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXH1 | NM_003923.3 | c.864T>C | p.Asn288= | synonymous_variant | 3/3 | ENST00000377317.5 | NP_003914.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXH1 | ENST00000377317.5 | c.864T>C | p.Asn288= | synonymous_variant | 3/3 | 1 | NM_003923.3 | ENSP00000366534 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000360 AC: 9AN: 250092Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135670
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460132Hom.: 0 Cov.: 35 AF XY: 0.0000124 AC XY: 9AN XY: 726382
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 34 AF XY: 0.0000404 AC XY: 3AN XY: 74318
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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