rs199594544
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004690.4(LATS1):c.2693C>T(p.Ala898Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,984 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251312Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135834
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461784Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727186
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2693C>T (p.A898V) alteration is located in exon 6 (coding exon 5) of the LATS1 gene. This alteration results from a C to T substitution at nucleotide position 2693, causing the alanine (A) at amino acid position 898 to be replaced by a valine (V). 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