3-129418447-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207307.3(EFCAB12):āc.488A>Gā(p.Lys163Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000025 in 1,602,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_207307.3 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
EFCAB12 | NM_207307.3 | c.488A>G | p.Lys163Arg | missense_variant, splice_region_variant | 3/9 | ENST00000505956.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB12 | ENST00000505956.6 | c.488A>G | p.Lys163Arg | missense_variant, splice_region_variant | 3/9 | 1 | NM_207307.3 | P1 | |
EFCAB12 | ENST00000503957.1 | c.38A>G | p.Lys13Arg | missense_variant, splice_region_variant | 2/4 | 5 | |||
EFCAB12 | ENST00000503498.1 | n.219A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/7 | 2 | ||||
EFCAB12 | ENST00000514900.5 | n.77A>G | non_coding_transcript_exon_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000222 AC: 5AN: 225674Hom.: 0 AF XY: 0.0000164 AC XY: 2AN XY: 122044
GnomAD4 exome AF: 0.0000152 AC: 22AN: 1450156Hom.: 0 Cov.: 31 AF XY: 0.0000139 AC XY: 10AN XY: 720304
GnomAD4 genome AF: 0.000118 AC: 18AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.488A>G (p.K163R) alteration is located in exon 3 (coding exon 3) of the EFCAB12 gene. This alteration results from a A to G substitution at nucleotide position 488, causing the lysine (K) at amino acid position 163 to be replaced by an arginine (R). 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