15-28272215-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_004667.6(HERC2):c.1083C>T(p.His361His) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,591,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004667.6 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HERC2 | NM_004667.6 | c.1083C>T | p.His361His | splice_region_variant, synonymous_variant | 9/93 | ENST00000261609.13 | NP_004658.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HERC2 | ENST00000261609.13 | c.1083C>T | p.His361His | splice_region_variant, synonymous_variant | 9/93 | 1 | NM_004667.6 | ENSP00000261609.8 | ||
HERC2 | ENST00000564734.5 | n.*953C>T | splice_region_variant, non_coding_transcript_exon_variant | 10/21 | 1 | ENSP00000456237.1 | ||||
HERC2 | ENST00000564734.5 | n.*953C>T | 3_prime_UTR_variant | 10/21 | 1 | ENSP00000456237.1 | ||||
HERC2 | ENST00000563670.1 | n.447C>T | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000934 AC: 234AN: 250436Hom.: 0 AF XY: 0.000835 AC XY: 113AN XY: 135348
GnomAD4 exome AF: 0.0000153 AC: 22AN: 1439604Hom.: 0 Cov.: 30 AF XY: 0.0000140 AC XY: 10AN XY: 714498
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 19, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | HERC2: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at