17-62407143-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000305286.8(EFCAB3):c.798G>A(p.Met266Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,672 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000305286.8 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFCAB3 | NM_173503.4 | c.798G>A | p.Met266Ile | missense_variant | 8/10 | ENST00000305286.8 | NP_775774.1 | |
EFCAB3 | NM_001144933.2 | c.954G>A | p.Met318Ile | missense_variant | 10/12 | NP_001138405.1 | ||
EFCAB3 | XM_011524381.3 | c.864G>A | p.Met288Ile | missense_variant | 8/10 | XP_011522683.2 | ||
EFCAB3 | XM_011524380.2 | c.798G>A | p.Met266Ile | missense_variant | 8/10 | XP_011522682.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EFCAB3 | ENST00000305286.8 | c.798G>A | p.Met266Ile | missense_variant | 8/10 | 1 | NM_173503.4 | ENSP00000302649 | P1 | |
EFCAB3 | ENST00000450662.7 | c.954G>A | p.Met318Ile | missense_variant | 10/12 | 5 | ENSP00000403932 | |||
EFCAB3 | ENST00000636041.1 | n.1183G>A | non_coding_transcript_exon_variant | 12/14 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249818Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 134966
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460520Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726540
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.954G>A (p.M318I) alteration is located in exon 10 (coding exon 10) of the EFCAB3 gene. This alteration results from a G to A substitution at nucleotide position 954, causing the methionine (M) at amino acid position 318 to be replaced by an isoleucine (I). 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