chr11-40114561-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001258419.2(LRRC4C):c.1732G>A(p.Asp578Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,613,990 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001258419.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC4C | NM_001258419.2 | c.1732G>A | p.Asp578Asn | missense_variant | 7/7 | ENST00000528697.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC4C | ENST00000528697.6 | c.1732G>A | p.Asp578Asn | missense_variant | 7/7 | 1 | NM_001258419.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251120Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135716
GnomAD4 exome AF: 0.000109 AC: 159AN: 1461880Hom.: 6 Cov.: 31 AF XY: 0.000100 AC XY: 73AN XY: 727242
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74294
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.1732G>A (p.D578N) alteration is located in exon 2 (coding exon 1) of the LRRC4C gene. This alteration results from a G to A substitution at nucleotide position 1732, causing the aspartic acid (D) at amino acid position 578 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