14-89931628-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145231.4(EFCAB11):c.323G>A(p.Arg108His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000812 in 1,613,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 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. R108C) has been classified as Uncertain significance.
Frequency
Consequence
NM_145231.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFCAB11 | NM_145231.4 | c.323G>A | p.Arg108His | missense_variant | 5/6 | ENST00000316738.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB11 | ENST00000316738.12 | c.323G>A | p.Arg108His | missense_variant | 5/6 | 2 | NM_145231.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 27AN: 250880Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135616
GnomAD4 exome AF: 0.0000808 AC: 118AN: 1461064Hom.: 1 Cov.: 30 AF XY: 0.0000977 AC XY: 71AN XY: 726842
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.323G>A (p.R108H) alteration is located in exon 5 (coding exon 5) of the EFCAB11 gene. This alteration results from a G to A substitution at nucleotide position 323, causing the arginine (R) at amino acid position 108 to be replaced by a histidine (H). 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