Variant 8-79765029-T-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 ENST00000354724.8(HEY1):c.*159A>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 0.745 in 541,088 control chromosomes in the GnomAD database, including 151,606 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 46693 hom., cov: 32)

Exomes 𝑓: 0.73 ( 104913 hom. )

Consequence

HEY1
ENST00000354724.8 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.05

Variant links:

Genes affected

HEY1 (HGNC:4880): (hes related family bHLH transcription factor with YRPW motif 1) This gene encodes a nuclear protein belonging to the hairy and enhancer of split-related (HESR) family of basic helix-loop-helix (bHLH)-type transcriptional repressors. Expression of this gene is induced by the Notch and c-Jun signal transduction pathways. Two similar and redundant genes in mouse are required for embryonic cardiovascular development, and are also implicated in neurogenesis and somitogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

HEY1 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=-0.86).

BP6

Variant 8-79765029-T-A is Benign according to our data. Variant chr8-79765029-T-A is described in ClinVar as [Benign]. Clinvar id is 1253254.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
HEY1	NM_012258.4 linkuse as main transcript	c.*159A>T	3_prime_UTR_variant	5/5	ENST00000354724.8	NP_036390.3
HEY1	NM_001040708.2 linkuse as main transcript	c.*159A>T	3_prime_UTR_variant	5/5		NP_001035798.1
HEY1	NM_001282851.2 linkuse as main transcript	c.*159A>T	3_prime_UTR_variant	2/2		NP_001269780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HEY1	ENST00000354724.8 linkuse as main transcript	c.*159A>T		3_prime_UTR_variant	5/5	1	NM_012258.4	ENSP00000346761	P1	Q9Y5J3-1

Frequencies

GnomAD3 genomes

AF:

0.778

AC:

118302

AN:

152076

Hom.:

46643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.908

Gnomad AMI

AF:

0.734

Gnomad AMR

AF:

0.774

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.785

Gnomad SAS

AF:

0.781

Gnomad FIN

AF:

0.727

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.713

Gnomad OTH

AF:

0.764

GnomAD4 exome

AF:

0.732

AC:

284739

AN:

388894

Hom.:

104913

Cov.:

AF XY:

0.731

AC XY:

144951

AN XY:

198252

show subpopulations

Gnomad4 AFR exome

AF:

0.906

Gnomad4 AMR exome

AF:

0.791

Gnomad4 ASJ exome

AF:

0.703

Gnomad4 EAS exome

AF:

0.791

Gnomad4 SAS exome

AF:

0.776

Gnomad4 FIN exome

AF:

0.723

Gnomad4 NFE exome

AF:

0.715

Gnomad4 OTH exome

AF:

0.737

GnomAD4 genome

AF:

0.778

AC:

118415

AN:

152194

Hom.:

46693

Cov.:

AF XY:

0.778

AC XY:

57897

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.907

Gnomad4 AMR

AF:

0.775

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.785

Gnomad4 SAS

AF:

0.782

Gnomad4 FIN

AF:

0.727

Gnomad4 NFE

AF:

0.713

Gnomad4 OTH

AF:

0.766

Alfa

AF:

0.751

Hom.:

5345

Bravo

AF:

0.789

Asia WGS

AF:

0.813

AC:

2825

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	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

DANN

Benign

0.61

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.

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