3-149183513-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000096.4(CP):c.2378G>A(p.Arg793His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00991 in 1,611,260 control chromosomes in the GnomAD database, including 104 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_000096.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CP | ENST00000264613.11 | c.2378G>A | p.Arg793His | missense_variant | Exon 13 of 19 | 1 | NM_000096.4 | ENSP00000264613.6 | ||
CP | ENST00000494544.1 | c.1727G>A | p.Arg576His | missense_variant | Exon 10 of 16 | 1 | ENSP00000420545.1 | |||
CP | ENST00000490639.5 | n.2410G>A | non_coding_transcript_exon_variant | Exon 13 of 17 | 1 | |||||
CP | ENST00000481169.5 | n.2165G>A | non_coding_transcript_exon_variant | Exon 12 of 18 | 2 | ENSP00000418773.1 |
Frequencies
GnomAD3 genomes AF: 0.0118 AC: 1794AN: 151636Hom.: 16 Cov.: 31
GnomAD3 exomes AF: 0.00731 AC: 1838AN: 251338Hom.: 15 AF XY: 0.00710 AC XY: 965AN XY: 135852
GnomAD4 exome AF: 0.00971 AC: 14175AN: 1459506Hom.: 88 Cov.: 31 AF XY: 0.00953 AC XY: 6922AN XY: 726084
GnomAD4 genome AF: 0.0118 AC: 1796AN: 151754Hom.: 16 Cov.: 31 AF XY: 0.0117 AC XY: 866AN XY: 74108
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 04, 2013 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Deficiency of ferroxidase Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2025 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 04, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 30, 2020 | This variant is associated with the following publications: (PMID: 15557511, 25758665, 26000822, 16150804) - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
CP-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 25, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at