chr17-8121643-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001165967.2(HES7):c.621G>A(p.Pro207=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000152 in 1,319,264 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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 8.6e-7 ( 0 hom. )
Consequence
HES7
NM_001165967.2 synonymous
NM_001165967.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0690
Genes affected
HES7 (HGNC:15977): (hes family bHLH transcription factor 7) This gene encodes a member of the hairy and enhancer of split family of bHLH transcription factors. The mouse ortholog of this gene is regulated by Notch signaling. The protein functions as a transcriptional repressor, and is implicated in correct patterning of the axial skeleton. A mutation in this gene has been shown to result in spondylocostal dysostosis. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 17-8121643-C-T is Benign according to our data. Variant chr17-8121643-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1534314.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.069 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HES7 | NM_001165967.2 | c.621G>A | p.Pro207= | synonymous_variant | 4/4 | ENST00000541682.7 | |
HES7 | NM_032580.4 | c.606G>A | p.Pro202= | synonymous_variant | 4/4 | ||
HES7 | XM_047436940.1 | c.717G>A | p.Pro239= | synonymous_variant | 3/3 | ||
HES7 | XM_047436941.1 | c.708G>A | p.Pro236= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HES7 | ENST00000541682.7 | c.621G>A | p.Pro207= | synonymous_variant | 4/4 | 1 | NM_001165967.2 | A1 | |
HES7 | ENST00000317814.8 | c.606G>A | p.Pro202= | synonymous_variant | 4/4 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151948Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 8.57e-7 AC: 1AN: 1167316Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 560528
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 151948Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74216
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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
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 13, 2022 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at