chr1-160813767-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002348.4(LY9):c.586C>A(p.Pro196Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 1,614,140 control chromosomes in the GnomAD database, including 230 homozygotes. 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 Benign (★).
Frequency
Genomes: 𝑓 0.0099 ( 13 hom., cov: 32)
Exomes 𝑓: 0.016 ( 217 hom. )
Consequence
LY9
NM_002348.4 missense
NM_002348.4 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: -5.70
Genes affected
LY9 (HGNC:6730): (lymphocyte antigen 9) LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0028006732).
BP6
?
Variant 1-160813767-C-A is Benign according to our data. Variant chr1-160813767-C-A is described in ClinVar as [Benign]. Clinvar id is 783299.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0156 (22841/1461874) while in subpopulation NFE AF= 0.0185 (20626/1112000). AF 95% confidence interval is 0.0183. There are 217 homozygotes in gnomad4_exome. There are 10840 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LY9 | NM_002348.4 | c.586C>A | p.Pro196Thr | missense_variant | 3/10 | ENST00000263285.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LY9 | ENST00000263285.11 | c.586C>A | p.Pro196Thr | missense_variant | 3/10 | 1 | NM_002348.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00993 AC: 1511AN: 152148Hom.: 13 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00935 AC: 2352AN: 251454Hom.: 19 AF XY: 0.00908 AC XY: 1234AN XY: 135894
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GnomAD4 exome AF: 0.0156 AC: 22841AN: 1461874Hom.: 217 Cov.: 31 AF XY: 0.0149 AC XY: 10840AN XY: 727236
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GnomAD4 genome ? AF: 0.00992 AC: 1510AN: 152266Hom.: 13 Cov.: 32 AF XY: 0.00971 AC XY: 723AN XY: 74450
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70
ESP6500AA
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18
ESP6500EA
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133
ExAC
?
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1029
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;N
MutationTaster
Benign
N;N;N;N;N;N;N
PrimateAI
Benign
T
REVEL
Benign
Sift4G
Benign
T;T;T
Polyphen
B;.;B
Vest4
MVP
MPC
0.072
ClinPred
T
GERP RS
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gMVP
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