Variant 8-79766297-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001282851.2(HEY1):c.-35delT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,517,660 control chromosomes in the GnomAD database, including 11,289 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1297 hom., cov: 31)

Exomes 𝑓: 0.11 ( 9992 hom. )

Consequence

HEY1
NM_001282851.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0850

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:

HEY1 (HGNC:):

HEY1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 8-79766297-CA-C is Benign according to our data. Variant chr8-79766297-CA-C is described in ClinVar as [Benign]. Clinvar id is 1221132.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
HEY1	NM_012258.4 linkuse as main transcript	c.331+353delT	intron_variant		ENST00000354724.8	NP_036390.3	Q9Y5J3-1
HEY1	NM_001282851.2 linkuse as main transcript	c.-35delT	5_prime_UTR_variant	1/2		NP_001269780.1	Q9Y5J3B4DEI9
HEY1	NM_001040708.2 linkuse as main transcript	c.343+353delT	intron_variant			NP_001035798.1	Q9Y5J3-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HEY1	ENST00000354724.8 linkuse as main transcript	c.331+353delT		intron_variant		1	NM_012258.4	ENSP00000346761.3		Q9Y5J3-1

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18838

AN:

151908

Hom.:

1302

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.0901

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.0522

AC:

5200

AN:

99616

Hom.:

214

AF XY:

0.0596

AC XY:

3241

AN XY:

54336

show subpopulations

Gnomad AFR exome

AF:

0.0299

Gnomad AMR exome

AF:

0.0211

Gnomad ASJ exome

AF:

0.107

Gnomad EAS exome

AF:

0.000106

Gnomad SAS exome

AF:

0.121

Gnomad FIN exome

AF:

0.0820

Gnomad NFE exome

AF:

0.0451

Gnomad OTH exome

AF:

0.0522

GnomAD4 exome

AF:

0.112

AC:

153568

AN:

1365634

Hom.:

9992

Cov.:

AF XY:

0.117

AC XY:

78606

AN XY:

673320

show subpopulations

Gnomad4 AFR exome

AF:

0.152

Gnomad4 AMR exome

AF:

0.0653

Gnomad4 ASJ exome

AF:

0.201

Gnomad4 EAS exome

AF:

0.000842

Gnomad4 SAS exome

AF:

0.241

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.125

GnomAD4 genome

AF:

0.124

AC:

18834

AN:

152026

Hom.:

1297

Cov.:

AF XY:

0.126

AC XY:

9398

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.0899

Gnomad4 ASJ

AF:

0.198

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.138

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.0788

Hom.:

149

Asia WGS

AF:

0.114

AC:

395

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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