11-124924816-C-T
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
Consequence
NM_152722.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HEPACAM | NM_152722.5 | c.339G>A | p.Gln113Gln | synonymous_variant | Exon 2 of 7 | ENST00000298251.5 | NP_689935.2 | |
HEPACAM | NM_001411043.1 | c.339G>A | p.Gln113Gln | synonymous_variant | Exon 2 of 7 | NP_001397972.1 | ||
HEPACAM | XM_005271449.3 | c.339G>A | p.Gln113Gln | synonymous_variant | Exon 2 of 7 | XP_005271506.1 | ||
LOC107984406 | XR_001748429.3 | n.335-18584C>T | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HEPACAM | ENST00000298251.5 | c.339G>A | p.Gln113Gln | synonymous_variant | Exon 2 of 7 | 1 | NM_152722.5 | ENSP00000298251.4 | ||
HEPACAM | ENST00000703807.1 | c.339G>A | p.Gln113Gln | synonymous_variant | Exon 2 of 7 | ENSP00000515485.1 | ||||
HEPACAM | ENST00000526273.1 | n.111G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
HEPACAM | ENST00000528971.1 | n.745G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0306 AC: 4659AN: 152126Hom.: 89 Cov.: 32
GnomAD3 exomes AF: 0.0334 AC: 8388AN: 251482Hom.: 237 AF XY: 0.0347 AC XY: 4713AN XY: 135918
GnomAD4 exome AF: 0.0277 AC: 40472AN: 1461876Hom.: 788 Cov.: 32 AF XY: 0.0286 AC XY: 20834AN XY: 727240
GnomAD4 genome AF: 0.0306 AC: 4661AN: 152244Hom.: 87 Cov.: 32 AF XY: 0.0300 AC XY: 2235AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
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Megalencephalic leukoencephalopathy with subcortical cysts Benign:1
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