2-237762860-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000392000.4(LRRFIP1):c.1147G>A(p.Glu383Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000752 in 1,461,894 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
ENST00000392000.4 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 |
---|---|---|---|---|---|---|---|
LRRFIP1 | NM_001137550.2 | c.1459+2655G>A | intron_variant | ENST00000308482.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRFIP1 | ENST00000308482.14 | c.1459+2655G>A | intron_variant | 1 | NM_001137550.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251456Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135896
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461894Hom.: 0 Cov.: 35 AF XY: 0.00000825 AC XY: 6AN XY: 727248
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.1147G>A (p.E383K) alteration is located in exon 11 (coding exon 11) of the LRRFIP1 gene. This alteration results from a G to A substitution at nucleotide position 1147, causing the glutamic acid (E) at amino acid position 383 to be replaced by a lysine (K). 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