8-22621522-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018688.6(BIN3):āc.662A>Gā(p.His221Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,613,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018688.6 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 | UniProt |
---|---|---|---|---|---|---|---|
BIN3 | NM_018688.6 | c.662A>G | p.His221Arg | missense_variant | 9/9 | ENST00000276416.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BIN3 | ENST00000276416.11 | c.662A>G | p.His221Arg | missense_variant | 9/9 | 1 | NM_018688.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246738Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134170
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461538Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727046
GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.662A>G (p.H221R) alteration is located in exon 9 (coding exon 9) of the BIN3 gene. This alteration results from a A to G substitution at nucleotide position 662, causing the histidine (H) at amino acid position 221 to be replaced by an arginine (R). 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