Variant 11-124919336-A-AAAAC details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001037558.4(HEPN1):c.-410_-407dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 199,830 control chromosomes in the GnomAD database, including 5,558 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4760 hom., cov: 25)

Exomes 𝑓: 0.15 ( 798 hom. )

Consequence

HEPN1
NM_001037558.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.736

Variant links:

Genes affected

HEPN1 (HGNC:34400): (hepatocellular carcinoma, down-regulated 1) This gene is expressed predominantly in the liver. Transient transfection studies show the expression of this gene significantly inhibits cell growth, suggesting a role for this gene in apoptosis. Expression of this gene is down-regulated or lost in hepatocellular carcinomas (HCC), suggesting that loss of this gene is involved in carcinogenesis of hepatocytes (PMID:12971969). This gene maps to the 3'-noncoding region of the HEPACAM gene (GeneID:220296) on the antisense strand. [provided by RefSeq, Aug 2020]

HEPN1 links:

HEPACAM (HGNC:26361): (hepatic and glial cell adhesion molecule) The protein encoded by this gene is a single-pass type I membrane protein that localizes to the cytoplasmic side of the cell membrane. The encoded protein acts as a homodimer and is involved in cell motility and cell-matrix interactions. The expression of this gene is downregulated or undetectable in many cancer cell lines, so this may be a tumor suppressor gene. [provided by RefSeq, Jul 2011]

HEPACAM links:

LOC107984406 (HGNC:):

LOC107984406 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-124919336-A-AAAAC is Benign according to our data. Variant chr11-124919336-A-AAAAC is described in ClinVar as [Benign]. Clinvar id is 303289.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
HEPN1	NM_001037558.4 linkuse as main transcript	c.-410_-407dup	5_prime_UTR_variant	1/1	ENST00000408930.7	NP_001032647.2
HEPACAM	NM_152722.5 linkuse as main transcript	c.1801_1802insGTTT	3_prime_UTR_variant	7/7	ENST00000298251.5	NP_689935.2
LOC107984406	XR_001748429.3 linkuse as main transcript	n.335-24059_335-24056dup	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HEPN1	ENST00000408930.7 linkuse as main transcript	c.-410_-407dup	5_prime_UTR_variant	1/1		NM_001037558.4	ENSP00000386143	P1
HEPACAM	ENST00000298251.5 linkuse as main transcript	c.1801_1802insGTTT	3_prime_UTR_variant	7/7	1	NM_152722.5	ENSP00000298251	P1	Q14CZ8-1
HEPACAM	ENST00000703807.1 linkuse as main transcript	c.1801_1802insGTTT	3_prime_UTR_variant	7/7			ENSP00000515485

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36372

AN:

151834

Hom.:

4749

Cov.:

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.0863

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.279

Gnomad MID

AF:

0.188

Gnomad NFE

AF:

0.199

Gnomad OTH

AF:

0.211

GnomAD4 exome

AF:

0.154

AC:

7378

AN:

47878

Hom.:

798

Cov.:

AF XY:

0.158

AC XY:

3755

AN XY:

23830

show subpopulations

Gnomad4 AFR exome

AF:

0.293

Gnomad4 AMR exome

AF:

0.0861

Gnomad4 ASJ exome

AF:

0.141

Gnomad4 EAS exome

AF:

0.0617

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.202

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.160

GnomAD4 genome

AF:

0.240

AC:

36419

AN:

151952

Hom.:

4760

Cov.:

AF XY:

0.240

AC XY:

17800

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.356

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.0858

Gnomad4 SAS

AF:

0.264

Gnomad4 FIN

AF:

0.279

Gnomad4 NFE

AF:

0.199

Gnomad4 OTH

AF:

0.210

Alfa

AF:

0.228

Hom.:

434

Bravo

AF:

0.231

Asia WGS

AF:

0.201

AC:

695

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Megalencephalic leukoencephalopathy with subcortical cysts

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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