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

Uncertain significance criteria provided, single submitter U:1

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

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsApr 08, 2024The c.563G>A (p.G188D) alteration is located in exon 4 (coding exon 4) of the HES7 gene. This alteration results from a G to A substitution at nucleotide position 563, causing the glycine (G) at amino acid position 188 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

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