11-124923786-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152722.5(HEPACAM):āc.652A>Gā(p.Met218Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 1,613,966 control chromosomes in the GnomAD database, including 415,256 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_152722.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HEPACAM | NM_152722.5 | c.652A>G | p.Met218Val | missense_variant | 3/7 | ENST00000298251.5 | NP_689935.2 | |
HEPACAM | NM_001411043.1 | c.652A>G | p.Met218Val | missense_variant | 3/7 | NP_001397972.1 | ||
HEPACAM | XM_005271449.3 | c.652A>G | p.Met218Val | missense_variant | 3/7 | XP_005271506.1 | ||
LOC107984406 | XR_001748429.3 | n.335-19614T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HEPACAM | ENST00000298251.5 | c.652A>G | p.Met218Val | missense_variant | 3/7 | 1 | NM_152722.5 | ENSP00000298251.4 | ||
HEPACAM | ENST00000703807.1 | c.652A>G | p.Met218Val | missense_variant | 3/7 | ENSP00000515485.1 | ||||
HEPACAM | ENST00000526273.1 | n.424A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.759 AC: 115386AN: 152108Hom.: 44366 Cov.: 32
GnomAD3 exomes AF: 0.722 AC: 181481AN: 251320Hom.: 66493 AF XY: 0.722 AC XY: 98113AN XY: 135816
GnomAD4 exome AF: 0.710 AC: 1037907AN: 1461740Hom.: 370838 Cov.: 60 AF XY: 0.711 AC XY: 516897AN XY: 727170
GnomAD4 genome AF: 0.759 AC: 115502AN: 152226Hom.: 44418 Cov.: 32 AF XY: 0.763 AC XY: 56781AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Megalencephalic leukoencephalopathy with subcortical cysts 2A Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without intellectual disability Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Megalencephalic leukoencephalopathy with subcortical cysts Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at