rs71377306
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_152347.5(EFCAB13):c.631C>T(p.Arg211*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,529,114 control chromosomes in the GnomAD database, including 3,898 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_152347.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EFCAB13 | ENST00000331493.7 | c.631C>T | p.Arg211* | stop_gained | Exon 9 of 25 | 1 | NM_152347.5 | ENSP00000332111.2 | ||
EFCAB13 | ENST00000517484.5 | c.517+2823C>T | intron_variant | Intron 8 of 21 | 2 | ENSP00000430048.1 | ||||
EFCAB13 | ENST00000517310.5 | c.73+2823C>T | intron_variant | Intron 9 of 10 | 2 | ENSP00000466136.1 | ||||
EFCAB13 | ENST00000520776.5 | n.651+2823C>T | intron_variant | Intron 6 of 13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0520 AC: 7896AN: 151978Hom.: 389 Cov.: 30
GnomAD3 exomes AF: 0.0737 AC: 17721AN: 240478Hom.: 1074 AF XY: 0.0763 AC XY: 9935AN XY: 130130
GnomAD4 exome AF: 0.0609 AC: 83832AN: 1377018Hom.: 3509 Cov.: 31 AF XY: 0.0623 AC XY: 42140AN XY: 676276
GnomAD4 genome AF: 0.0518 AC: 7884AN: 152096Hom.: 389 Cov.: 30 AF XY: 0.0558 AC XY: 4146AN XY: 74330
ClinVar
Submissions by phenotype
EFCAB13-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at