1-89583939-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001369817.2(LRRC8B):āc.1289A>Gā(p.Asn430Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,614,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001369817.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC8B | NM_001369817.2 | c.1289A>G | p.Asn430Ser | missense_variant | 5/6 | ENST00000330947.7 | |
LRRC8B | NM_001134476.2 | c.1289A>G | p.Asn430Ser | missense_variant | 7/8 | ||
LRRC8B | NM_001369819.2 | c.1289A>G | p.Asn430Ser | missense_variant | 6/7 | ||
LRRC8B | NM_015350.4 | c.1289A>G | p.Asn430Ser | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC8B | ENST00000330947.7 | c.1289A>G | p.Asn430Ser | missense_variant | 5/6 | 5 | NM_001369817.2 | P1 | |
LRRC8C-DT | ENST00000655657.3 | n.701-515T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000215 AC: 54AN: 250630Hom.: 0 AF XY: 0.000229 AC XY: 31AN XY: 135518
GnomAD4 exome AF: 0.000155 AC: 227AN: 1461872Hom.: 0 Cov.: 34 AF XY: 0.000168 AC XY: 122AN XY: 727230
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74502
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at