chr7-150337603-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142928.2(LRRC61):c.742C>G(p.Leu248Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000277 in 1,551,004 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001142928.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC61 | NM_001142928.2 | c.742C>G | p.Leu248Val | missense_variant | 3/3 | ENST00000359623.9 | |
LRRC61 | NM_001363433.1 | c.742C>G | p.Leu248Val | missense_variant | 3/3 | ||
LRRC61 | NM_001363434.1 | c.742C>G | p.Leu248Val | missense_variant | 3/3 | ||
LRRC61 | NM_023942.3 | c.742C>G | p.Leu248Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC61 | ENST00000359623.9 | c.742C>G | p.Leu248Val | missense_variant | 3/3 | 2 | NM_001142928.2 | P1 | |
LRRC61 | ENST00000323078.7 | c.742C>G | p.Leu248Val | missense_variant | 2/2 | 1 | P1 | ||
ENST00000647589.1 | n.117+4C>G | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | |||||||
LRRC61 | ENST00000493307.1 | c.742C>G | p.Leu248Val | missense_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000154 AC: 3AN: 195088Hom.: 0 AF XY: 0.00000943 AC XY: 1AN XY: 106004
GnomAD4 exome AF: 0.0000300 AC: 42AN: 1398778Hom.: 0 Cov.: 32 AF XY: 0.0000362 AC XY: 25AN XY: 689962
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2022 | The c.742C>G (p.L248V) alteration is located in exon 3 (coding exon 1) of the LRRC61 gene. This alteration results from a C to G substitution at nucleotide position 742, causing the leucine (L) at amino acid position 248 to be replaced by a valine (V). 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