rs104894766
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM5PP5BP4BS2
The NM_005448.2(BMP15):c.226C>T(p.Arg76Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000178 in 1,193,726 control chromosomes in the GnomAD database, including 1 homozygotes. There are 114 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R76H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_005448.2 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 |
---|---|---|---|---|---|---|---|
BMP15 | NM_005448.2 | c.226C>T | p.Arg76Cys | missense_variant | 1/2 | ENST00000252677.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP15 | ENST00000252677.4 | c.226C>T | p.Arg76Cys | missense_variant | 1/2 | 1 | NM_005448.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000321 AC: 36AN: 112258Hom.: 0 Cov.: 24 AF XY: 0.000581 AC XY: 20AN XY: 34438
GnomAD3 exomes AF: 0.000413 AC: 62AN: 150151Hom.: 0 AF XY: 0.000699 AC XY: 32AN XY: 45781
GnomAD4 exome AF: 0.000164 AC: 177AN: 1081412Hom.: 1 Cov.: 33 AF XY: 0.000267 AC XY: 94AN XY: 352434
GnomAD4 genome ? AF: 0.000321 AC: 36AN: 112314Hom.: 0 Cov.: 24 AF XY: 0.000580 AC XY: 20AN XY: 34504
ClinVar
Submissions by phenotype
Ovarian dysgenesis 2 Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Sep 12, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Premature ovarian failure 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at