chr4-81046086-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001201.5(BMP3):c.665C>T(p.Thr222Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,614,156 control chromosomes in the GnomAD database, including 189 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T222A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001201.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP3 | NM_001201.5 | c.665C>T | p.Thr222Met | missense_variant | 2/3 | ENST00000282701.4 | |
BMP3 | XM_006714291.4 | c.665C>T | p.Thr222Met | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP3 | ENST00000282701.4 | c.665C>T | p.Thr222Met | missense_variant | 2/3 | 1 | NM_001201.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0196 AC: 2986AN: 152200Hom.: 99 Cov.: 32
GnomAD3 exomes AF: 0.00618 AC: 1550AN: 250748Hom.: 34 AF XY: 0.00525 AC XY: 711AN XY: 135478
GnomAD4 exome AF: 0.00286 AC: 4178AN: 1461838Hom.: 92 Cov.: 34 AF XY: 0.00276 AC XY: 2007AN XY: 727216
GnomAD4 genome ? AF: 0.0196 AC: 2988AN: 152318Hom.: 97 Cov.: 32 AF XY: 0.0198 AC XY: 1474AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at