rs9624808

Positions:

• chr22-25374065-G-A
• chr22-25374065-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007068030.1(LRP5L):​n.1966C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,020 control chromosomes in the GnomAD database, including 1,118 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 0.11 (1118 hom., cov: 32)
• Consequence: LRP5L XR_007068030.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

LRP5L (HGNC:):

ACMG classification

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 = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRP5L	XR_007068030.1	n.1966C>T		non_coding_transcript_exon_variant	4/7
LRP5L	XR_007068031.1	n.2218C>T		non_coding_transcript_exon_variant	3/6
LRP5L	XR_005228024.2	n.601+1748C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290796	ENST00000444995.7	n.570+1748C>T		intron_variant		5
ENSG00000290796	ENST00000468442.1	n.347+1748C>T		intron_variant		3
ENSG00000290796	ENST00000650168.1	n.702+103C>T		intron_variant
LRP5L	ENST00000650500.2	n.599+103C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16962 AN: 151904 Hom.: 1111 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0817

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.112 AC: 16987 AN: 152020 Hom.: 1118 Cov.: 32 AF XY: 0.111 AC XY: 8284 AN XY: 74342

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0770

Gnomad4 ASJ AF: 0.0817

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.116 Hom.: 193

Bravo AF: 0.103

Asia WGS AF: 0.0410 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9624808; hg19: chr22-25770032;