14-89797247-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145231.4(EFCAB11):c.488C>T(p.Ala163Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,612,892 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
NM_145231.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFCAB11 | NM_145231.4 | c.488C>T | p.Ala163Val | missense_variant | 6/6 | ENST00000316738.12 | |
EFCAB11 | NM_001284269.2 | c.416C>T | p.Ala139Val | missense_variant | 6/6 | ||
EFCAB11 | NM_001284267.2 | c.344C>T | p.Ala115Val | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB11 | ENST00000316738.12 | c.488C>T | p.Ala163Val | missense_variant | 6/6 | 2 | NM_145231.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152022Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000877 AC: 22AN: 250970Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135684
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1460752Hom.: 0 Cov.: 30 AF XY: 0.0000908 AC XY: 66AN XY: 726770
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.488C>T (p.A163V) alteration is located in exon 6 (coding exon 6) of the EFCAB11 gene. This alteration results from a C to T substitution at nucleotide position 488, causing the alanine (A) at amino acid position 163 to be replaced by a valine (V). 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