10-7720904-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002216.3(ITIH2):c.679C>T(p.Pro227Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002216.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITIH2 | ENST00000358415.9 | c.679C>T | p.Pro227Ser | missense_variant | Exon 7 of 21 | 1 | NM_002216.3 | ENSP00000351190.4 | ||
ITIH2 | ENST00000379587.4 | c.646C>T | p.Pro216Ser | missense_variant | Exon 6 of 20 | 5 | ENSP00000368906.3 | |||
ITIH2 | ENST00000429820.5 | c.604C>T | p.Pro202Ser | missense_variant | Exon 6 of 7 | 3 | ENSP00000388826.1 | |||
ITIH2 | ENST00000480387.1 | n.*3C>T | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251476Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461580Hom.: 0 Cov.: 29 AF XY: 0.00000550 AC XY: 4AN XY: 727120
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.679C>T (p.P227S) alteration is located in exon 7 (coding exon 7) of the ITIH2 gene. This alteration results from a C to T substitution at nucleotide position 679, causing the proline (P) at amino acid position 227 to be replaced by a serine (S). 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