chr6-35462914-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_021922.3(FANCE):c.1509C>T(p.Asn503=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000496 in 1,614,156 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_021922.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCE | NM_021922.3 | c.1509C>T | p.Asn503= | splice_region_variant, synonymous_variant | 9/10 | ENST00000229769.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCE | ENST00000229769.3 | c.1509C>T | p.Asn503= | splice_region_variant, synonymous_variant | 9/10 | 1 | NM_021922.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000334 AC: 84AN: 251478Hom.: 2 AF XY: 0.000324 AC XY: 44AN XY: 135920
GnomAD4 exome AF: 0.000524 AC: 766AN: 1461796Hom.: 16 Cov.: 32 AF XY: 0.000512 AC XY: 372AN XY: 727184
GnomAD4 genome AF: 0.000230 AC: 35AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74504
ClinVar
Submissions by phenotype
Fanconi anemia complementation group E Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at