NM_014572.3:c.2660G>A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_014572.3(LATS2):c.2660G>A(p.Arg887His) variant causes a missense change. The variant allele was found at a frequency of 0.000057 in 1,612,628 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R887R) has been classified as Benign.
Frequency
Consequence
NM_014572.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LATS2 | NM_014572.3 | c.2660G>A | p.Arg887His | missense_variant | Exon 6 of 8 | ENST00000382592.5 | NP_055387.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 249684Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 134984
GnomAD4 exome AF: 0.0000596 AC: 87AN: 1460430Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 726496
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2660G>A (p.R887H) alteration is located in exon 6 (coding exon 5) of the LATS2 gene. This alteration results from a G to A substitution at nucleotide position 2660, causing the arginine (R) at amino acid position 887 to be replaced by a histidine (H). 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