6-149679896-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004690.4(LATS1):c.2572G>A(p.Asp858Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000181 in 1,602,616 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 AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000289 AC: 7AN: 242330Hom.: 0 AF XY: 0.0000457 AC XY: 6AN XY: 131294
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1450474Hom.: 0 Cov.: 31 AF XY: 0.0000250 AC XY: 18AN XY: 721104
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2572G>A (p.D858N) alteration is located in exon 5 (coding exon 4) of the LATS1 gene. This alteration results from a G to A substitution at nucleotide position 2572, causing the aspartic acid (D) at amino acid position 858 to be replaced by an asparagine (N). 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