17-8121649-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001165967.2(HES7):āc.615A>Gā(p.Pro205=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000495 in 1,313,502 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 0.000026 ( 0 hom., cov: 32)
Exomes š: 0.000052 ( 0 hom. )
Consequence
HES7
NM_001165967.2 synonymous
NM_001165967.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.63
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 17-8121649-T-C is Benign according to our data. Variant chr17-8121649-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1607264.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.63 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HES7 | NM_001165967.2 | c.615A>G | p.Pro205= | synonymous_variant | 4/4 | ENST00000541682.7 | |
HES7 | NM_032580.4 | c.600A>G | p.Pro200= | synonymous_variant | 4/4 | ||
HES7 | XM_047436940.1 | c.711A>G | p.Pro237= | synonymous_variant | 3/3 | ||
HES7 | XM_047436941.1 | c.702A>G | p.Pro234= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HES7 | ENST00000541682.7 | c.615A>G | p.Pro205= | synonymous_variant | 4/4 | 1 | NM_001165967.2 | A1 | |
HES7 | ENST00000317814.8 | c.600A>G | p.Pro200= | synonymous_variant | 4/4 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151268Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
4
AN:
151268
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000525 AC: 61AN: 1162234Hom.: 0 Cov.: 30 AF XY: 0.0000502 AC XY: 28AN XY: 557774
GnomAD4 exome
AF:
AC:
61
AN:
1162234
Hom.:
Cov.:
30
AF XY:
AC XY:
28
AN XY:
557774
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000264 AC: 4AN: 151268Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73856
GnomAD4 genome
AF:
AC:
4
AN:
151268
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
73856
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
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 | Invitae | Sep 21, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at