rs16388

Variant names:

• chr22-25354849-G-GGGCAA
• ENST00000402785.2:n.536-38_536-37insTTGCC

Your query was ambiguous. Multiple possible variants found:

• chr22-25354849-G-GGGCAA
• chr22-25354849-G-GGGCAAT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000402785.2(ENSG00000290796):​n.536-38_536-37insTTGCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 34)
• Consequence: ENSG00000290796 ENST00000402785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

ENSG00000290796 (HGNC:):

LRP5L (HGNC:25323): (LDL receptor related protein 5 like (pseudogene)) Predicted to enable coreceptor activity. Predicted to be involved in several processes, including animal organ development; cholesterol homeostasis; and osteoblast development. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRP5L	XR_005228024.2	n.3339-38_3339-37insTTGCC		intron_variant	Intron 5 of 6
LRP5L	XR_005228030.2	n.1171-38_1171-37insTTGCC		intron_variant	Intron 5 of 6
LRP5L	XR_007068026.1	n.1171-38_1171-37insTTGCC		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290796	ENST00000402785.2	n.536-38_536-37insTTGCC		intron_variant	Intron 2 of 3	1
ENSG00000290796	ENST00000467672.5	n.2904-38_2904-37insTTGCC		intron_variant	Intron 2 of 3	1
ENSG00000290796	ENST00000444995.7	n.1140-38_1140-37insTTGCC		intron_variant	Intron 5 of 6	5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-25750816;