rs1499511

Variant names:

• chr11-36066303-T-C
• rs1499511
• NM_174902.4:c.194-15350T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_174902.4(LDLRAD3):​c.194-15350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,870 control chromosomes in the GnomAD database, including 34,852 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 0.67 (34852 hom., cov: 30)
• Consequence: LDLRAD3 NM_174902.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 5 publications found

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]

LOC101928510 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDLRAD3	NM_174902.4	c.194-15350T>C		intron_variant	Intron 2 of 5	ENST00000315571.6	NP_777562.1
LOC101928510	NR_135064.1	n.1116A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LDLRAD3	NM_001304263.2	c.47-15350T>C		intron_variant	Intron 1 of 4		NP_001291192.1
LDLRAD3	NM_001304264.2	c.-286-15350T>C		intron_variant	Intron 1 of 5		NP_001291193.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDLRAD3	ENST00000315571.6	c.194-15350T>C		intron_variant	Intron 2 of 5	1	NM_174902.4	ENSP00000318607.5
LDLRAD3	ENST00000528989.5	c.47-15350T>C		intron_variant	Intron 1 of 4	1		ENSP00000433954.1
LDLRAD3	ENST00000524419.5	c.47-15350T>C		intron_variant	Intron 1 of 5	5		ENSP00000434313.1
LDLRAD3	ENST00000532490.1	n.148-15350T>C		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101375 AN: 151752 Hom.: 34804 Cov.: 30

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.637

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.668 AC: 101483 AN: 151870 Hom.: 34852 Cov.: 30 AF XY: 0.667 AC XY: 49493 AN XY: 74206

African (AFR) AF: 0.845 AC: 34978 AN: 41412

American (AMR) AF: 0.647 AC: 9858 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3466

East Asian (EAS) AF: 0.645 AC: 3321 AN: 5148

South Asian (SAS) AF: 0.631 AC: 3032 AN: 4806

European-Finnish (FIN) AF: 0.621 AC: 6530 AN: 10522

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39660 AN: 67954

Other (OTH) AF: 0.636 AC: 1341 AN: 2108

Alfa AF: 0.604 Hom.: 46868

Bravo AF: 0.677

Asia WGS AF: 0.676 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1499511; hg19: chr11-36087853;