7-128029608-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000249363.4(LRRC4):āc.1033C>Gā(p.Gln345Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,613,936 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (ā ).
Frequency
Consequence
ENST00000249363.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC4 | NM_022143.5 | c.1033C>G | p.Gln345Glu | missense_variant | 2/2 | ENST00000249363.4 | NP_071426.1 | |
SND1 | NM_014390.4 | c.1779+38552G>C | intron_variant | ENST00000354725.8 | NP_055205.2 | |||
LRRC4 | XM_011516461.4 | c.1033C>G | p.Gln345Glu | missense_variant | 3/3 | XP_011514763.1 | ||
LRRC4 | XM_047420695.1 | c.1033C>G | p.Gln345Glu | missense_variant | 3/3 | XP_047276651.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC4 | ENST00000249363.4 | c.1033C>G | p.Gln345Glu | missense_variant | 2/2 | 1 | NM_022143.5 | ENSP00000249363 | P1 | |
SND1 | ENST00000354725.8 | c.1779+38552G>C | intron_variant | 1 | NM_014390.4 | ENSP00000346762 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000426 AC: 107AN: 251016Hom.: 0 AF XY: 0.000420 AC XY: 57AN XY: 135756
GnomAD4 exome AF: 0.000240 AC: 351AN: 1461752Hom.: 1 Cov.: 33 AF XY: 0.000241 AC XY: 175AN XY: 727168
GnomAD4 genome AF: 0.000230 AC: 35AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.1033C>G (p.Q345E) alteration is located in exon 2 (coding exon 1) of the LRRC4 gene. This alteration results from a C to G substitution at nucleotide position 1033, causing the glutamine (Q) at amino acid position 345 to be replaced by a glutamic acid (E). 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