8-79766065-C-CA

Variant summary

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

The ENST00000354724.8(HEY1):​c.332-295_332-294insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 713,632 control chromosomes in the GnomAD database, including 66,281 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 15118 hom., cov: 0)
Exomes 𝑓: 0.42 ( 51163 hom. )

Consequence

HEY1
ENST00000354724.8 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.72
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 8-79766065-C-CA is Benign according to our data. Variant chr8-79766065-C-CA is described in ClinVar as [Benign]. Clinvar id is 1220652.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HEY1NM_012258.4 linkuse as main transcriptc.332-295_332-294insT intron_variant ENST00000354724.8 NP_036390.3
HEY1NM_001040708.2 linkuse as main transcriptc.344-295_344-294insT intron_variant NP_001035798.1
HEY1NM_001282851.2 linkuse as main transcriptc.61+137_61+138insT intron_variant NP_001269780.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HEY1ENST00000354724.8 linkuse as main transcriptc.332-295_332-294insT intron_variant 1 NM_012258.4 ENSP00000346761 P1Q9Y5J3-1

Frequencies

GnomAD3 genomes
AF:
0.443
AC:
67375
AN:
151938
Hom.:
15109
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.488
Gnomad AMI
AF:
0.491
Gnomad AMR
AF:
0.487
Gnomad ASJ
AF:
0.316
Gnomad EAS
AF:
0.490
Gnomad SAS
AF:
0.416
Gnomad FIN
AF:
0.402
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.420
Gnomad OTH
AF:
0.399
GnomAD4 exome
AF:
0.421
AC:
236486
AN:
561576
Hom.:
51163
AF XY:
0.420
AC XY:
122443
AN XY:
291470
show subpopulations
Gnomad4 AFR exome
AF:
0.488
Gnomad4 AMR exome
AF:
0.504
Gnomad4 ASJ exome
AF:
0.316
Gnomad4 EAS exome
AF:
0.477
Gnomad4 SAS exome
AF:
0.423
Gnomad4 FIN exome
AF:
0.387
Gnomad4 NFE exome
AF:
0.419
Gnomad4 OTH exome
AF:
0.411
GnomAD4 genome
AF:
0.443
AC:
67419
AN:
152056
Hom.:
15118
Cov.:
0
AF XY:
0.443
AC XY:
32962
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.487
Gnomad4 AMR
AF:
0.487
Gnomad4 ASJ
AF:
0.316
Gnomad4 EAS
AF:
0.491
Gnomad4 SAS
AF:
0.419
Gnomad4 FIN
AF:
0.402
Gnomad4 NFE
AF:
0.420
Gnomad4 OTH
AF:
0.396
Alfa
AF:
0.263
Hom.:
500

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 submitterclinical testingGeneDxNov 12, 2018- -

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.

Other links and lift over

dbSNP: rs11448857; hg19: chr8-80678300; API