chr1-53343358-T-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792371.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRP8-DT	ENST00000792371.1		n.227+12107T>C		intron	N/A
	ENSG00000226938	ENST00000792492.1		n.80-373A>G		intron	N/A
	ENSG00000226938	ENST00000792493.1		n.291-373A>G		intron	N/A

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 v4.9

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;