3-52816983-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002218.5(ITIH4):c.2372T>C(p.Leu791Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,613,840 control chromosomes in the GnomAD database, including 5,169 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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_002218.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITIH4 | NM_002218.5 | c.2372T>C | p.Leu791Pro | missense_variant | 21/24 | ENST00000266041.9 | |
ITIH4 | NM_001166449.2 | c.2282T>C | p.Leu761Pro | missense_variant | 19/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITIH4 | ENST00000266041.9 | c.2372T>C | p.Leu791Pro | missense_variant | 21/24 | 1 | NM_002218.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.101 AC: 15434AN: 152078Hom.: 2645 Cov.: 33
GnomAD3 exomes AF: 0.0263 AC: 6613AN: 251340Hom.: 1075 AF XY: 0.0195 AC XY: 2648AN XY: 135834
GnomAD4 exome AF: 0.0107 AC: 15598AN: 1461646Hom.: 2512 Cov.: 32 AF XY: 0.00927 AC XY: 6739AN XY: 727138
GnomAD4 genome ? AF: 0.102 AC: 15471AN: 152194Hom.: 2657 Cov.: 33 AF XY: 0.0983 AC XY: 7316AN XY: 74414
ClinVar
Submissions by phenotype
ITIH4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 06, 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