rs9694676

Variant names:

• chr8-104588948-A-C
• NM_013437.5:c.-51T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-104588948-A-C
• chr8-104588948-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_013437.5(LRP12):​c.-51T>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000082 in 1,220,124 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 8.2e-7 (0 hom.)
• Consequence: LRP12 NM_013437.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727

Genes affected

LRP12 (HGNC:31708): (LDL receptor related protein 12) This gene encodes a member of the low-density lipoprotein receptor related protein family. The product of this gene is a transmembrane protein that is differentially expressed in many cancer cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRP12	NM_013437.5	c.-51T>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 7	ENST00000276654.10	NP_038465.1
LRP12	NM_013437.5	c.-51T>G		5_prime_UTR_variant	Exon 1 of 7	ENST00000276654.10	NP_038465.1
LRP12	NM_001135703.3	c.-51T>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 6		NP_001129175.1
LRP12	NM_001135703.3	c.-51T>G		5_prime_UTR_variant	Exon 1 of 6		NP_001129175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP12	ENST00000276654.10	c.-51T>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 7	1	NM_013437.5	ENSP00000276654.5
LRP12	ENST00000276654.10	c.-51T>G		5_prime_UTR_variant	Exon 1 of 7	1	NM_013437.5	ENSP00000276654.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.20e-7 AC: 1 AN: 1220124 Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0 AN XY: 610304

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000301

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	17
DANN	Benign	0.71

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-105601176;