rs262421
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_174902.4(LDLRAD3):c.47-19294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,126 control chromosomes in the GnomAD database, including 15,581 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 0.43 ( 15581 hom., cov: 33)
Consequence
LDLRAD3
NM_174902.4 intron
NM_174902.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.875
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=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LDLRAD3 | NM_174902.4 | c.47-19294C>T | intron_variant | ENST00000315571.6 | |||
LDLRAD3 | NM_001304263.2 | c.47-64844C>T | intron_variant | ||||
LDLRAD3 | NM_001304264.2 | c.-286-64844C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LDLRAD3 | ENST00000315571.6 | c.47-19294C>T | intron_variant | 1 | NM_174902.4 | P1 | |||
LDLRAD3 | ENST00000528989.5 | c.47-64844C>T | intron_variant | 1 | |||||
LDLRAD3 | ENST00000524419.5 | c.47-64844C>T | intron_variant | 5 | |||||
LDLRAD3 | ENST00000532490.1 | n.147+15623C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.430 AC: 65373AN: 152008Hom.: 15575 Cov.: 33
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.430 AC: 65396AN: 152126Hom.: 15581 Cov.: 33 AF XY: 0.427 AC XY: 31750AN XY: 74352
GnomAD4 genome
?
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31750
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74352
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1209
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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