NM_152722.5:c.339G>A

Variant names:

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_152722.5(HEPACAM):c.339G>A(p.Gln113Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 1,614,120 control chromosomes in the GnomAD database, including 875 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 87 hom., cov: 32)

Exomes 𝑓: 0.028 ( 788 hom. )

Consequence

HEPACAM
NM_152722.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 1.71

Variant links:

Genes affected

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 11-124924816-C-T is Benign according to our data. Variant chr11-124924816-C-T is described in ClinVar as [Benign]. Clinvar id is 262677.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.71 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HEPACAM	NM_152722.5 link	c.339G>A	p.Gln113Gln	synonymous_variant	Exon 2 of 7	ENST00000298251.5	NP_689935.2	Q14CZ8-1
HEPACAM	NM_001411043.1 link	c.339G>A	p.Gln113Gln	synonymous_variant	Exon 2 of 7		NP_001397972.1
HEPACAM	XM_005271449.3 link	c.339G>A	p.Gln113Gln	synonymous_variant	Exon 2 of 7		XP_005271506.1
LOC107984406	XR_001748429.3 link	n.335-18584C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
HEPACAM	ENST00000298251.5 link	c.339G>A	p.Gln113Gln	synonymous_variant	Exon 2 of 7	1	NM_152722.5	ENSP00000298251.4	Q14CZ8-1
HEPACAM	ENST00000703807.1 link	c.339G>A	p.Gln113Gln	synonymous_variant	Exon 2 of 7			ENSP00000515485.1	A0A994J4I1
HEPACAM	ENST00000526273.1 link	n.111G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
HEPACAM	ENST00000528971.1 link	n.745G>A		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0306

AC:

4659

AN:

152126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0420

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0185

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.0799

Gnomad SAS

AF:

0.0621

Gnomad FIN

AF:

0.00697

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0228

Gnomad OTH

AF:

0.0287

GnomAD3 exomes

AF:

0.0334

AC:

8388

AN:

251482

Hom.:

237

AF XY:

0.0347

AC XY:

4713

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.0419

Gnomad AMR exome

AF:

0.0175

Gnomad ASJ exome

AF:

0.0608

Gnomad EAS exome

AF:

0.0919

Gnomad SAS exome

AF:

0.0569

Gnomad FIN exome

AF:

0.00827

Gnomad NFE exome

AF:

0.0238

Gnomad OTH exome

AF:

0.0279

GnomAD4 exome

AF:

0.0277

AC:

40472

AN:

1461876

Hom.:

788

Cov.:

AF XY:

0.0286

AC XY:

20834

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.0443

Gnomad4 AMR exome

AF:

0.0175

Gnomad4 ASJ exome

AF:

0.0610

Gnomad4 EAS exome

AF:

0.0826

Gnomad4 SAS exome

AF:

0.0547

Gnomad4 FIN exome

AF:

0.00874

Gnomad4 NFE exome

AF:

0.0233

Gnomad4 OTH exome

AF:

0.0321

GnomAD4 genome

AF:

0.0306

AC:

4661

AN:

152244

Hom.:

Cov.:

AF XY:

0.0300

AC XY:

2235

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0420

Gnomad4 AMR

AF:

0.0185

Gnomad4 ASJ

AF:

0.0608

Gnomad4 EAS

AF:

0.0801

Gnomad4 SAS

AF:

0.0615

Gnomad4 FIN

AF:

0.00697

Gnomad4 NFE

AF:

0.0228

Gnomad4 OTH

AF:

0.0284

Alfa

AF:

0.0284

Hom.:

Bravo

AF:

0.0327

Asia WGS

AF:

0.0460

AC:

162

AN:

3478

EpiCase

AF:

0.0220

EpiControl

AF:

0.0241

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 31, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Megalencephalic leukoencephalopathy with subcortical cysts

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

7.7

DANN

Benign

0.87

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