rs12361738
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_174902.4(LDLRAD3):c.194-6234G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,968 control chromosomes in the GnomAD database, including 15,702 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.45 ( 15702 hom., cov: 32)
Consequence
LDLRAD3
NM_174902.4 intron
NM_174902.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.883
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LDLRAD3 | NM_174902.4 | c.194-6234G>C | intron_variant | ENST00000315571.6 | |||
LOC101928510 | NR_135064.1 | n.157+2326C>G | intron_variant, non_coding_transcript_variant | ||||
LDLRAD3 | NM_001304263.2 | c.47-6234G>C | intron_variant | ||||
LDLRAD3 | NM_001304264.2 | c.-286-6234G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDLRAD3 | ENST00000315571.6 | c.194-6234G>C | intron_variant | 1 | NM_174902.4 | P1 | |||
LDLRAD3 | ENST00000528989.5 | c.47-6234G>C | intron_variant | 1 | |||||
LDLRAD3 | ENST00000524419.5 | c.47-6234G>C | intron_variant | 5 | |||||
LDLRAD3 | ENST00000532490.1 | n.148-6234G>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.452 AC: 68634AN: 151848Hom.: 15678 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.452 AC: 68704AN: 151968Hom.: 15702 Cov.: 32 AF XY: 0.453 AC XY: 33627AN XY: 74260
GnomAD4 genome
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32
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33627
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1364
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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