rs11680012
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000392000.4(LRRFIP1):āc.2069G>Cā(p.Arg690Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 1,614,196 control chromosomes in the GnomAD database, including 1,618 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000392000.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRFIP1 | NM_001137550.2 | c.1459+3577G>C | intron_variant | ENST00000308482.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRFIP1 | ENST00000308482.14 | c.1459+3577G>C | intron_variant | 1 | NM_001137550.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0332 AC: 5046AN: 152212Hom.: 103 Cov.: 32
GnomAD3 exomes AF: 0.0389 AC: 9772AN: 251000Hom.: 237 AF XY: 0.0402 AC XY: 5449AN XY: 135708
GnomAD4 exome AF: 0.0438 AC: 64042AN: 1461866Hom.: 1515 Cov.: 35 AF XY: 0.0439 AC XY: 31910AN XY: 727232
GnomAD4 genome ? AF: 0.0331 AC: 5043AN: 152330Hom.: 103 Cov.: 32 AF XY: 0.0327 AC XY: 2438AN XY: 74496
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at