chr13-43882356-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_153218.4(LACC1):c.734G>A(p.Arg245Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000935 in 1,604,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153218.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LACC1 | NM_153218.4 | c.734G>A | p.Arg245Gln | missense_variant | 3/7 | ENST00000325686.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LACC1 | ENST00000325686.7 | c.734G>A | p.Arg245Gln | missense_variant | 3/7 | 1 | NM_153218.4 | P1 | |
LACC1 | ENST00000441843.5 | c.734G>A | p.Arg245Gln | missense_variant | 3/7 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000480 AC: 73AN: 151968Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000140 AC: 34AN: 242614Hom.: 0 AF XY: 0.0000992 AC XY: 13AN XY: 131004
GnomAD4 exome AF: 0.0000509 AC: 74AN: 1452554Hom.: 0 Cov.: 30 AF XY: 0.0000471 AC XY: 34AN XY: 722234
GnomAD4 genome ? AF: 0.000500 AC: 76AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.000444 AC XY: 33AN XY: 74334
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.734G>A (p.R245Q) alteration is located in exon 3 (coding exon 2) of the LACC1 gene. This alteration results from a G to A substitution at nucleotide position 734, causing the arginine (R) at amino acid position 245 to be replaced by a glutamine (Q). 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