1-89583529-G-A
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001369817.2(LRRC8B):c.879G>A(p.Val293=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00405 in 1,612,836 control chromosomes in the GnomAD database, including 222 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.022 ( 112 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 110 hom. )
Consequence
LRRC8B
NM_001369817.2 synonymous
NM_001369817.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0630
Genes affected
LRRC8B (HGNC:30692): (leucine rich repeat containing 8 VRAC subunit B) Contributes to volume-sensitive anion channel activity. Involved in anion transmembrane transport. Located in cytoplasm and plasma membrane. Is integral component of plasma membrane. Part of ion channel complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 1-89583529-G-A is Benign according to our data. Variant chr1-89583529-G-A is described in ClinVar as [Benign]. Clinvar id is 780245.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.063 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC8B | NM_001369817.2 | c.879G>A | p.Val293= | synonymous_variant | 5/6 | ENST00000330947.7 | |
LRRC8B | NM_001134476.2 | c.879G>A | p.Val293= | synonymous_variant | 7/8 | ||
LRRC8B | NM_001369819.2 | c.879G>A | p.Val293= | synonymous_variant | 6/7 | ||
LRRC8B | NM_015350.4 | c.879G>A | p.Val293= | synonymous_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC8B | ENST00000330947.7 | c.879G>A | p.Val293= | synonymous_variant | 5/6 | 5 | NM_001369817.2 | P1 | |
LRRC8C-DT | ENST00000655657.3 | n.701-105C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0215 AC: 3278AN: 152142Hom.: 111 Cov.: 32
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GnomAD3 exomes AF: 0.00566 AC: 1415AN: 250130Hom.: 45 AF XY: 0.00404 AC XY: 546AN XY: 135306
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GnomAD4 exome AF: 0.00223 AC: 3255AN: 1460576Hom.: 110 Cov.: 34 AF XY: 0.00191 AC XY: 1386AN XY: 726682
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GnomAD4 genome AF: 0.0216 AC: 3282AN: 152260Hom.: 112 Cov.: 32 AF XY: 0.0205 AC XY: 1527AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at