rs61746895
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020937.4(FANCM):āc.229A>Gā(p.Thr77Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 1,613,858 control chromosomes in the GnomAD database, including 235 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_020937.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FANCM | NM_020937.4 | c.229A>G | p.Thr77Ala | missense_variant | 1/23 | ENST00000267430.10 | NP_065988.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FANCM | ENST00000267430.10 | c.229A>G | p.Thr77Ala | missense_variant | 1/23 | 1 | NM_020937.4 | ENSP00000267430.5 |
Frequencies
GnomAD3 genomes AF: 0.0188 AC: 2851AN: 151862Hom.: 34 Cov.: 32
GnomAD3 exomes AF: 0.0116 AC: 2902AN: 251226Hom.: 42 AF XY: 0.0112 AC XY: 1516AN XY: 135800
GnomAD4 exome AF: 0.0147 AC: 21457AN: 1461880Hom.: 202 Cov.: 32 AF XY: 0.0143 AC XY: 10366AN XY: 727240
GnomAD4 genome AF: 0.0188 AC: 2858AN: 151978Hom.: 33 Cov.: 32 AF XY: 0.0171 AC XY: 1270AN XY: 74264
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Mar 26, 2021 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 25, 2021 | This variant is associated with the following publications: (PMID: 29351780, 19737859) - |
Premature ovarian failure 15 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Fanconi anemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at