chr17-8121686-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PM2BP4

The NM_001165967.2(HES7):​c.578G>A​(p.Gly193Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G193S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

HES7
NM_001165967.2 missense

Scores

2
3
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.58
Variant links:
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 Uncertain_significance. Variant got 3 ACMG points.

PM1
In a chain Transcription factor HES-7 (size 224) in uniprot entity HES7_HUMAN there are 5 pathogenic changes around while only 1 benign (83%) in NM_001165967.2
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.31250602).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HES7NM_001165967.2 linkuse as main transcriptc.578G>A p.Gly193Asp missense_variant 4/4 ENST00000541682.7
HES7NM_032580.4 linkuse as main transcriptc.563G>A p.Gly188Asp missense_variant 4/4
HES7XM_047436940.1 linkuse as main transcriptc.674G>A p.Gly225Asp missense_variant 3/3
HES7XM_047436941.1 linkuse as main transcriptc.665G>A p.Gly222Asp missense_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HES7ENST00000541682.7 linkuse as main transcriptc.578G>A p.Gly193Asp missense_variant 4/41 NM_001165967.2 A1Q9BYE0-2
HES7ENST00000317814.8 linkuse as main transcriptc.563G>A p.Gly188Asp missense_variant 4/41 P4Q9BYE0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
0.00088
T
BayesDel_noAF
Benign
-0.24
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.21
.;T
Eigen
Benign
0.13
Eigen_PC
Benign
0.13
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Benign
0.53
T;T
M_CAP
Pathogenic
0.92
D
MetaRNN
Benign
0.31
T;T
MetaSVM
Benign
-0.59
T
MutationAssessor
Benign
0.69
.;N
MutationTaster
Benign
0.64
N;N
PrimateAI
Pathogenic
0.89
D
PROVEAN
Benign
-1.6
N;N
REVEL
Benign
0.28
Sift
Benign
0.22
T;T
Sift4G
Uncertain
0.039
D;D
Polyphen
0.96
.;D
Vest4
0.21
MutPred
0.22
.;Gain of loop (P = 0.0435);
MVP
0.58
MPC
2.1
ClinPred
0.82
D
GERP RS
4.1
Varity_R
0.14
gMVP
0.21

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.

Other links and lift over

dbSNP: rs1981333577; hg19: chr17-8025004; API