rs2074613
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001945.3(HBEGF):c.555-231G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 583,366 control chromosomes in the GnomAD database, including 91,959 homozygotes. 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: 𝑓 0.60 ( 27672 hom., cov: 32)
Exomes 𝑓: 0.54 ( 64287 hom. )
Consequence
HBEGF
NM_001945.3 intron
NM_001945.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.09
Genes affected
HBEGF (HGNC:3059): (heparin binding EGF like growth factor) Enables growth factor activity and heparin binding activity. Involved in several processes, including epidermal growth factor receptor signaling pathway; positive regulation of protein kinase B signaling; and positive regulation of wound healing. Located in cell surface and extracellular space. Implicated in glomerulosclerosis and perinatal necrotizing enterocolitis. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HBEGF | NM_001945.3 | c.555-231G>A | intron_variant | ENST00000230990.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBEGF | ENST00000230990.7 | c.555-231G>A | intron_variant | 1 | NM_001945.3 | P1 | |||
HBEGF | ENST00000482211.2 | n.152G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.596 AC: 90544AN: 151906Hom.: 27653 Cov.: 32
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GnomAD4 exome AF: 0.543 AC: 234327AN: 431340Hom.: 64287 Cov.: 0 AF XY: 0.541 AC XY: 123096AN XY: 227538
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GnomAD4 genome ? AF: 0.596 AC: 90598AN: 152026Hom.: 27672 Cov.: 32 AF XY: 0.591 AC XY: 43956AN XY: 74318
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at