chr8-22098559-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022749.7(FHIP2B):c.905G>A(p.Arg302Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000894 in 1,610,202 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★).
Frequency
Consequence
NM_022749.7 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 |
---|---|---|---|---|---|---|---|
FHIP2B | NM_022749.7 | c.905G>A | p.Arg302Gln | missense_variant | 7/17 | ENST00000289921.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FHIP2B | ENST00000289921.8 | c.905G>A | p.Arg302Gln | missense_variant | 7/17 | 5 | NM_022749.7 | P1 | |
FHIP2B | ENST00000450006.7 | c.905G>A | p.Arg302Gln | missense_variant, NMD_transcript_variant | 7/18 | 1 | |||
FHIP2B | ENST00000464226.2 | n.654G>A | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152042Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000258 AC: 62AN: 240436Hom.: 0 AF XY: 0.000305 AC XY: 40AN XY: 131012
GnomAD4 exome AF: 0.0000912 AC: 133AN: 1458042Hom.: 2 Cov.: 40 AF XY: 0.000105 AC XY: 76AN XY: 725010
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74392
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 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