rs2782497

Variant names:

• chr1-53343358-T-C
• rs2782497
• ENST00000792371.1:n.227+12107T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000792371.1(LRP8-DT):​n.227+12107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,984 control chromosomes in the GnomAD database, including 10,285 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 0.36 (10285 hom., cov: 32)
• Consequence: LRP8-DT ENST00000792371.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795
• Publications: 3 publications found

Genes affected

LRP8-DT (HGNC:52561): (LRP8 divergent transcript)

ENSG00000226938 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378731	XR_001738057.2	n.73-373A>G		intron_variant	Intron 1 of 3
LOC105378731	XR_007066092.1	n.73-373A>G		intron_variant	Intron 1 of 4
LOC105378731	XR_007066093.1	n.73-373A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP8-DT	ENST00000792371.1	n.227+12107T>C		intron_variant	Intron 2 of 2
ENSG00000226938	ENST00000792492.1	n.80-373A>G		intron_variant	Intron 1 of 3
ENSG00000226938	ENST00000792493.1	n.291-373A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54259 AN: 151866 Hom.: 10278 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.357 AC: 54294 AN: 151984 Hom.: 10285 Cov.: 32 AF XY: 0.355 AC XY: 26372 AN XY: 74286

African (AFR) AF: 0.492 AC: 20345 AN: 41388

American (AMR) AF: 0.276 AC: 4213 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1196 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1778 AN: 5158

South Asian (SAS) AF: 0.343 AC: 1648 AN: 4800

European-Finnish (FIN) AF: 0.276 AC: 2919 AN: 10578

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21085 AN: 67986

Other (OTH) AF: 0.329 AC: 696 AN: 2116

Alfa AF: 0.323 Hom.: 5448

Bravo AF: 0.364

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.79
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2782497; hg19: chr1-53809030;