chr12-56083757-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS1
The NM_001982.4(ERBB3):c.89C>T(p.Pro30Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,614,048 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERBB3 | NM_001982.4 | c.89C>T | p.Pro30Leu | missense_variant | 2/28 | ENST00000267101.8 | |
ERBB3 | NM_001005915.1 | c.89C>T | p.Pro30Leu | missense_variant | 2/3 | ||
ERBB3 | XM_047428500.1 | c.-89C>T | 5_prime_UTR_variant | 2/28 | |||
ERBB3 | XM_047428501.1 | c.-89C>T | 5_prime_UTR_variant | 2/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERBB3 | ENST00000267101.8 | c.89C>T | p.Pro30Leu | missense_variant | 2/28 | 1 | NM_001982.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00236 AC: 359AN: 152078Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00227 AC: 572AN: 251490Hom.: 1 AF XY: 0.00229 AC XY: 311AN XY: 135918
GnomAD4 exome AF: 0.00172 AC: 2514AN: 1461852Hom.: 7 Cov.: 31 AF XY: 0.00179 AC XY: 1305AN XY: 727222
GnomAD4 genome ? AF: 0.00236 AC: 359AN: 152196Hom.: 1 Cov.: 32 AF XY: 0.00245 AC XY: 182AN XY: 74418
ClinVar
Submissions by phenotype
ERBB3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 29, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | ERBB3: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at