1-70038181-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_001370785.2(LRRC7):c.2357C>T(p.Pro786Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370785.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC7 | NM_001370785.2 | c.2357C>T | p.Pro786Leu | missense_variant | 21/27 | ENST00000651989.2 | |
LRRC7-AS1 | XR_001738107.2 | n.946G>A | non_coding_transcript_exon_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC7 | ENST00000651989.2 | c.2357C>T | p.Pro786Leu | missense_variant | 21/27 | NM_001370785.2 | P1 | ||
LRRC7 | ENST00000415775.2 | c.95C>T | p.Pro32Leu | missense_variant | 15/21 | 1 | |||
LRRC7 | ENST00000310961.9 | c.2258C>T | p.Pro753Leu | missense_variant | 22/27 | 5 | |||
LRRC7 | ENST00000651217.1 | n.2273C>T | non_coding_transcript_exon_variant | 19/25 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250904Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135542
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727202
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2022 | The c.2243C>T (p.P748L) alteration is located in exon 19 (coding exon 19) of the LRRC7 gene. This alteration results from a C to T substitution at nucleotide position 2243, causing the proline (P) at amino acid position 748 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