7-128029244-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_022143.5(LRRC4):c.1397C>T(p.Pro466Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,020 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 (★).
Frequency
Consequence
NM_022143.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC4 | NM_022143.5 | c.1397C>T | p.Pro466Leu | missense_variant | 2/2 | ENST00000249363.4 | NP_071426.1 | |
SND1 | NM_014390.4 | c.1779+38188G>A | intron_variant | ENST00000354725.8 | NP_055205.2 | |||
LRRC4 | XM_011516461.4 | c.1397C>T | p.Pro466Leu | missense_variant | 3/3 | XP_011514763.1 | ||
LRRC4 | XM_047420695.1 | c.1397C>T | p.Pro466Leu | missense_variant | 3/3 | XP_047276651.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC4 | ENST00000249363.4 | c.1397C>T | p.Pro466Leu | missense_variant | 2/2 | 1 | NM_022143.5 | ENSP00000249363 | P1 | |
SND1 | ENST00000354725.8 | c.1779+38188G>A | intron_variant | 1 | NM_014390.4 | ENSP00000346762 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251444Hom.: 1 AF XY: 0.0000441 AC XY: 6AN XY: 135902
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461872Hom.: 1 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727236
GnomAD4 genome AF: 0.000118 AC: 18AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.1397C>T (p.P466L) alteration is located in exon 2 (coding exon 1) of the LRRC4 gene. This alteration results from a C to T substitution at nucleotide position 1397, causing the proline (P) at amino acid position 466 to be replaced by a leucine (L). 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