chr12-56101214-A-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_001982.4(ERBB3):c.3355A>T(p.Ser1119Cys) variant causes a missense change. The variant allele was found at a frequency of 0.106 in 1,613,498 control chromosomes in the GnomAD database, including 9,756 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001982.4 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERBB3 | NM_001982.4 | c.3355A>T | p.Ser1119Cys | missense_variant | 27/28 | ENST00000267101.8 | NP_001973.2 | |
ERBB3 | XM_047428500.1 | c.3178A>T | p.Ser1060Cys | missense_variant | 27/28 | XP_047284456.1 | ||
ERBB3 | XM_047428501.1 | c.3178A>T | p.Ser1060Cys | missense_variant | 27/28 | XP_047284457.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERBB3 | ENST00000267101.8 | c.3355A>T | p.Ser1119Cys | missense_variant | 27/28 | 1 | NM_001982.4 | ENSP00000267101.4 |
Frequencies
GnomAD3 genomes AF: 0.0952 AC: 14437AN: 151688Hom.: 726 Cov.: 30
GnomAD3 exomes AF: 0.0888 AC: 22324AN: 251316Hom.: 1153 AF XY: 0.0904 AC XY: 12280AN XY: 135840
GnomAD4 exome AF: 0.107 AC: 156263AN: 1461692Hom.: 9029 Cov.: 34 AF XY: 0.106 AC XY: 77018AN XY: 727148
GnomAD4 genome AF: 0.0951 AC: 14444AN: 151806Hom.: 727 Cov.: 30 AF XY: 0.0952 AC XY: 7061AN XY: 74208
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2019 | This variant is associated with the following publications: (PMID: 30071039) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at