chr1-63454895-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014288.5(ITGB3BP):c.328A>G(p.Ile110Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000188 in 1,491,668 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 Uncertain significance (★).
Frequency
Consequence
NM_014288.5 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 |
---|---|---|---|---|---|---|---|
ITGB3BP | NM_014288.5 | c.328A>G | p.Ile110Val | missense_variant | 5/9 | ENST00000271002.15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB3BP | ENST00000271002.15 | c.328A>G | p.Ile110Val | missense_variant | 5/9 | 1 | NM_014288.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000204 AC: 5AN: 245588Hom.: 0 AF XY: 0.00000753 AC XY: 1AN XY: 132826
GnomAD4 exome AF: 0.00000971 AC: 13AN: 1339368Hom.: 0 Cov.: 21 AF XY: 0.00000743 AC XY: 5AN XY: 672724
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.445A>G (p.I149V) alteration is located in exon 6 (coding exon 6) of the ITGB3BP gene. This alteration results from a A to G substitution at nucleotide position 445, causing the isoleucine (I) at amino acid position 149 to be replaced by a valine (V). 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