17-47283410-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000212.3(ITGB3):āc.222C>Gā(p.Asn74Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000212.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGB3 | NM_000212.3 | c.222C>G | p.Asn74Lys | missense_variant | 3/15 | ENST00000559488.7 | NP_000203.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGB3 | ENST00000559488.7 | c.222C>G | p.Asn74Lys | missense_variant | 3/15 | 1 | NM_000212.3 | ENSP00000452786.2 | ||
ITGB3 | ENST00000571680.1 | c.222C>G | p.Asn74Lys | missense_variant | 3/9 | 1 | ENSP00000461626.1 | |||
ENSG00000259753 | ENST00000560629.1 | n.186C>G | non_coding_transcript_exon_variant | 3/18 | 2 | ENSP00000456711.2 | ||||
ITGB3 | ENST00000696963.1 | c.222C>G | p.Asn74Lys | missense_variant | 3/14 | ENSP00000513002.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461888Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727242
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 01, 2024 | The c.222C>G (p.N74K) alteration is located in exon 3 (coding exon 3) of the ITGB3 gene. This alteration results from a C to G substitution at nucleotide position 222, causing the asparagine (N) at amino acid position 74 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