Variant chr17-8121490-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001165967.2(HES7):c.*81G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,215,036 control chromosomes in the GnomAD database, including 6,770 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1368 hom., cov: 32)

Exomes 𝑓: 0.098 ( 5402 hom. )

Consequence

HES7
NM_001165967.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.635

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]

HES7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 17-8121490-C-A is Benign according to our data. Variant chr17-8121490-C-A is described in ClinVar as [Benign]. Clinvar id is 1291988.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
HES7	NM_001165967.2 linkuse as main transcript	c.*81G>T	3_prime_UTR_variant	4/4	ENST00000541682.7
HES7	NM_032580.4 linkuse as main transcript	c.*81G>T	3_prime_UTR_variant	4/4
HES7	XM_047436940.1 linkuse as main transcript	c.*81G>T	3_prime_UTR_variant	3/3
HES7	XM_047436941.1 linkuse as main transcript	c.*81G>T	3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HES7	ENST00000541682.7 linkuse as main transcript	c.*81G>T		3_prime_UTR_variant	4/4	1	NM_001165967.2	A1	Q9BYE0-2

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18893

AN:

152128

Hom.:

1367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.161

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0920

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.0785

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.0931

Gnomad OTH

AF:

0.128

GnomAD4 exome

AF:

0.0982

AC:

104390

AN:

1062794

Hom.:

5402

Cov.:

AF XY:

0.0987

AC XY:

49861

AN XY:

504992

show subpopulations

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.0995

Gnomad4 ASJ exome

AF:

0.166

Gnomad4 EAS exome

AF:

0.0954

Gnomad4 SAS exome

AF:

0.115

Gnomad4 FIN exome

AF:

0.0880

Gnomad4 NFE exome

AF:

0.0938

Gnomad4 OTH exome

AF:

0.109

GnomAD4 genome

AF:

0.124

AC:

18902

AN:

152242

Hom.:

1368

Cov.:

AF XY:

0.125

AC XY:

9268

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.191

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.166

Gnomad4 EAS

AF:

0.0923

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.0785

Gnomad4 NFE

AF:

0.0931

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.0941

Hom.:

598

Bravo

AF:

0.130

Asia WGS

AF:

0.117

AC:

406

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 20, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.71

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over