6-149683201-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004690.4(LATS1):c.1888C>T(p.Arg630Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000178 in 1,461,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004690.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251322Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135842
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461726Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727170
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1888C>T (p.R630C) alteration is located in exon 4 (coding exon 3) of the LATS1 gene. This alteration results from a C to T substitution at nucleotide position 1888, causing the arginine (R) at amino acid position 630 to be replaced by a cysteine (C). 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