chr10-7566178-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030569.7(ITIH5):c.2379C>A(p.Asn793Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030569.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITIH5 | NM_030569.7 | c.2379C>A | p.Asn793Lys | missense_variant | 13/14 | ENST00000397146.7 | |
ITIH5 | NM_032817.6 | c.1737C>A | p.Asn579Lys | missense_variant | 9/10 | ||
ITIH5 | XM_011519713.4 | c.2454C>A | p.Asn818Lys | missense_variant | 14/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITIH5 | ENST00000397146.7 | c.2379C>A | p.Asn793Lys | missense_variant | 13/14 | 1 | NM_030569.7 | P1 | |
ITIH5 | ENST00000613909.4 | c.1737C>A | p.Asn579Lys | missense_variant | 9/10 | 1 | |||
ITIH5 | ENST00000473591.1 | n.641C>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251264Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135840
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461848Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727214
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.2379C>A (p.N793K) alteration is located in exon 13 (coding exon 13) of the ITIH5 gene. This alteration results from a C to A substitution at nucleotide position 2379, causing the asparagine (N) at amino acid position 793 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at