1-46684513-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014774.3(EFCAB14):c.1164G>T(p.Arg388Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014774.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFCAB14 | NM_014774.3 | c.1164G>T | p.Arg388Ser | missense_variant | Exon 9 of 11 | ENST00000371933.8 | NP_055589.1 | |
EFCAB14-AS1 | NR_038827.1 | n.269-2160C>A | intron_variant | Intron 2 of 3 | ||||
EFCAB14-AS1 | NR_038828.1 | n.185-2160C>A | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461784Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727198
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1164G>T (p.R388S) alteration is located in exon 9 (coding exon 9) of the EFCAB14 gene. This alteration results from a G to T substitution at nucleotide position 1164, causing the arginine (R) at amino acid position 388 to be replaced by a serine (S). 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