chr1-226735684-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002221.4(ITPKB):c.1775A>G(p.Asn592Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,605,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. N592N) has been classified as Benign.
Frequency
Consequence
NM_002221.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPKB | NM_002221.4 | c.1775A>G | p.Asn592Ser | missense_variant | 2/8 | ENST00000429204.6 | |
ITPKB | NM_001388404.1 | c.1775A>G | p.Asn592Ser | missense_variant | 2/3 | ||
ITPKB | XM_017001211.3 | c.1775A>G | p.Asn592Ser | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPKB | ENST00000429204.6 | c.1775A>G | p.Asn592Ser | missense_variant | 2/8 | 5 | NM_002221.4 | P1 | |
ITPKB | ENST00000272117.8 | c.1775A>G | p.Asn592Ser | missense_variant | 2/8 | 1 | P1 | ||
ITPKB | ENST00000366784.1 | c.1775A>G | p.Asn592Ser | missense_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000737 AC: 18AN: 244086Hom.: 0 AF XY: 0.0000681 AC XY: 9AN XY: 132092
GnomAD4 exome AF: 0.0000998 AC: 145AN: 1453572Hom.: 0 Cov.: 34 AF XY: 0.000112 AC XY: 81AN XY: 722414
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74284
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at