chrX-50915837-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PP3_ModerateBP6BS2
The NM_005448.2(BMP15):c.409T>A(p.Tyr137Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000306 in 1,209,607 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005448.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP15 | NM_005448.2 | c.409T>A | p.Tyr137Asn | missense_variant | 2/2 | ENST00000252677.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP15 | ENST00000252677.4 | c.409T>A | p.Tyr137Asn | missense_variant | 2/2 | 1 | NM_005448.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000188 AC: 21AN: 111518Hom.: 0 Cov.: 23 AF XY: 0.000178 AC XY: 6AN XY: 33688
GnomAD3 exomes AF: 0.0000710 AC: 13AN: 182977Hom.: 0 AF XY: 0.0000592 AC XY: 4AN XY: 67511
GnomAD4 exome AF: 0.0000146 AC: 16AN: 1098089Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363453
GnomAD4 genome ? AF: 0.000188 AC: 21AN: 111518Hom.: 0 Cov.: 23 AF XY: 0.000178 AC XY: 6AN XY: 33688
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.409T>A (p.Y137N) alteration is located in exon 2 (coding exon 2) of the BMP15 gene. This alteration results from a T to A substitution at nucleotide position 409, causing the tyrosine (Y) at amino acid position 137 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
BMP15-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 27, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at