rs875989813
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_020937.4(FANCM):c.1397-16_1397-15delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000152 in 1,314,968 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
FANCM
NM_020937.4 intron
NM_020937.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.514
Publications
0 publications found
Genes affected
FANCM (HGNC:23168): (FA complementation group M) The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group M. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
FANCM Gene-Disease associations (from GenCC):
- Fanconi anemiaInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: G2P, Orphanet
- spermatogenic failure 28Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- male infertility with azoospermia or oligozoospermia due to single gene mutationInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- breast cancerInheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000118 AC: 2AN: 168802 AF XY: 0.0000109 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
168802
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000152 AC: 2AN: 1314968Hom.: 0 AF XY: 0.00000152 AC XY: 1AN XY: 656338 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1314968
Hom.:
AF XY:
AC XY:
1
AN XY:
656338
show subpopulations
African (AFR)
AF:
AC:
1
AN:
28558
American (AMR)
AF:
AC:
0
AN:
36408
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24104
East Asian (EAS)
AF:
AC:
0
AN:
35262
South Asian (SAS)
AF:
AC:
0
AN:
73252
European-Finnish (FIN)
AF:
AC:
0
AN:
49024
Middle Eastern (MID)
AF:
AC:
1
AN:
4360
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1009456
Other (OTH)
AF:
AC:
0
AN:
54544
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.400
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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