Genetic Variant NM_152722.5:c.*862C>T (chr11-124920276-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_152722.5(HEPACAM):c.*862C>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 0.00000228 in 877,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.0000023 ( 0 hom. )

Consequence

HEPACAM
NM_152722.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28

Publications

0 publications found

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:

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:

ENSG00000254943 (HGNC:):

ENSG00000254943 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152722.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HEPACAM	NM_152722.5	MANE Select	c.*862C>T	3_prime_UTR	Exon 7 of 7	NP_689935.2	Q14CZ8-1
HEPN1	NM_001037558.4	MANE Select	c.*259G>A	3_prime_UTR	Exon 1 of 1	NP_001032647.2	Q6WQI6
HEPACAM	NM_001411043.1		c.*862C>T	3_prime_UTR	Exon 7 of 7	NP_001397972.1	A0A994J4I1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HEPACAM	ENST00000298251.5	TSL:1 MANE Select	c.*862C>T	3_prime_UTR	Exon 7 of 7	ENSP00000298251.4	Q14CZ8-1
HEPN1	ENST00000408930.7	TSL:6 MANE Select	c.*259G>A	3_prime_UTR	Exon 1 of 1	ENSP00000386143.4	Q6WQI6
HEPACAM	ENST00000703807.1		c.*862C>T	3_prime_UTR	Exon 7 of 7	ENSP00000515485.1	A0A994J4I1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000228

AC:

AN:

877350

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

439678

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

20396

American (AMR)

AF:

0.00

AC:

AN:

23538

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17258

East Asian (EAS)

AF:

0.00

AC:

AN:

32826

South Asian (SAS)

AF:

0.00

AC:

AN:

56688

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45164

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4442

European-Non Finnish (NFE)

AF:

0.00000314

AC:

AN:

637268

Other (OTH)

AF:

0.00

AC:

AN:

39770

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.0

(source)

DANN

Benign

0.68

PhyloP100

-2.3

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over