11-36227278-G-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_174902.4(LDLRAD3):c.648G>A(p.Leu216=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
LDLRAD3
NM_174902.4 synonymous
NM_174902.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.44
Genes affected
LDLRAD3 (HGNC:27046): (low density lipoprotein receptor class A domain containing 3) Predicted to enable amyloid-beta binding activity. Predicted to act upstream of or within receptor-mediated endocytosis and regulation of protein processing. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 11-36227278-G-A is Benign according to our data. Variant chr11-36227278-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2681372.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1.44 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LDLRAD3 | NM_174902.4 | c.648G>A | p.Leu216= | synonymous_variant | 5/6 | ENST00000315571.6 | |
LDLRAD3 | NM_001304263.2 | c.501G>A | p.Leu167= | synonymous_variant | 4/5 | ||
LDLRAD3 | NM_001304264.2 | c.285G>A | p.Leu95= | synonymous_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDLRAD3 | ENST00000315571.6 | c.648G>A | p.Leu216= | synonymous_variant | 5/6 | 1 | NM_174902.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249190Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134968
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461800Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727202
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GnomAD4 genome Cov.: 33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
EBV-positive nodal T- and NK-cell lymphoma Benign:1
Likely benign, no assertion criteria provided | research | Department of Clinical Pathology, School of Medicine, Fujita Health University | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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