chr8-91127127-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001129890.2(LRRC69):āc.350A>Gā(p.Asn117Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000245 in 1,548,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 31)
Exomes š: 0.000026 ( 0 hom. )
Consequence
LRRC69
NM_001129890.2 missense
NM_001129890.2 missense
Scores
6
5
8
Clinical Significance
Conservation
PhyloP100: 5.35
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.752
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC69 | NM_001129890.2 | c.350A>G | p.Asn117Ser | missense_variant | 3/8 | ENST00000448384.3 | NP_001123362.1 | |
LRRC69 | NM_001354470.2 | c.183+24283A>G | intron_variant | NP_001341399.1 | ||||
LRRC69 | NR_148895.2 | n.595A>G | non_coding_transcript_exon_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC69 | ENST00000448384.3 | c.350A>G | p.Asn117Ser | missense_variant | 3/8 | 5 | NM_001129890.2 | ENSP00000400803 | P1 | |
LRRC69 | ENST00000343709.7 | c.183+24283A>G | intron_variant | 2 | ENSP00000343221 | |||||
LRRC69 | ENST00000520099.5 | c.*342A>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/11 | 2 | ENSP00000428537 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000139 AC: 21AN: 150934Hom.: 0 AF XY: 0.000125 AC XY: 10AN XY: 80234
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GnomAD4 exome AF: 0.0000265 AC: 37AN: 1396682Hom.: 0 Cov.: 30 AF XY: 0.0000232 AC XY: 16AN XY: 688956
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74240
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.350A>G (p.N117S) alteration is located in exon 3 (coding exon 3) of the LRRC69 gene. This alteration results from a A to G substitution at nucleotide position 350, causing the asparagine (N) at amino acid position 117 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at