chr14-89931629-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_145231.4(EFCAB11):c.322C>T(p.Arg108Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000383 in 1,460,682 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R108H) has been classified as Uncertain significance.
Frequency
Consequence
NM_145231.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFCAB11 | NM_145231.4 | c.322C>T | p.Arg108Cys | missense_variant, splice_region_variant | 5/6 | ENST00000316738.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB11 | ENST00000316738.12 | c.322C>T | p.Arg108Cys | missense_variant, splice_region_variant | 5/6 | 2 | NM_145231.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250684Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135538
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1460682Hom.: 0 Cov.: 29 AF XY: 0.0000372 AC XY: 27AN XY: 726684
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.322C>T (p.R108C) alteration is located in exon 5 (coding exon 5) of the EFCAB11 gene. This alteration results from a C to T substitution at nucleotide position 322, causing the arginine (R) at amino acid position 108 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at