chr9-130924239-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032843.5(FIBCD1):c.710C>A(p.Thr237Asn) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,590,384 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 18/23 in silico tools predict 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_032843.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FIBCD1 | NM_032843.5 | c.710C>A | p.Thr237Asn | missense_variant, splice_region_variant | 3/7 | ENST00000372338.9 | |
FIBCD1 | NM_001145106.2 | c.710C>A | p.Thr237Asn | missense_variant, splice_region_variant | 4/8 | ||
FIBCD1 | XM_047423989.1 | c.710C>A | p.Thr237Asn | missense_variant, splice_region_variant | 4/8 | ||
FIBCD1 | XM_047423990.1 | c.236C>A | p.Thr79Asn | missense_variant, splice_region_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FIBCD1 | ENST00000372338.9 | c.710C>A | p.Thr237Asn | missense_variant, splice_region_variant | 3/7 | 1 | NM_032843.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000190 AC: 4AN: 210034Hom.: 0 AF XY: 0.0000260 AC XY: 3AN XY: 115488
GnomAD4 exome AF: 0.00000834 AC: 12AN: 1438142Hom.: 0 Cov.: 32 AF XY: 0.00000701 AC XY: 5AN XY: 713132
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74444
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at