12-59148374-G-A

Variant names:

• chr12-59148374-G-A
• rs1500038
• ENST00000716010.1:n.327-41418G>A

Variant summary

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

The ENST00000716010.1(LRIG3-DT):​n.327-41418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 151,636 control chromosomes in the GnomAD database, including 52,604 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 0.83 (52604 hom., cov: 28)
• Consequence: LRIG3-DT ENST00000716010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 1 publications found

Genes affected

LRIG3-DT (HGNC:55476): (LRIG3 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716010.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRIG3-DT	ENST00000716010.1		n.327-41418G>A		intron	N/A
	LRIG3-DT	ENST00000804556.1		n.470-16558G>A		intron	N/A
	LRIG3-DT	ENST00000804557.1		n.497-16558G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126064 AN: 151520 Hom.: 52565 Cov.: 28

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.832 AC: 126159 AN: 151636 Hom.: 52604 Cov.: 28 AF XY: 0.832 AC XY: 61614 AN XY: 74016

African (AFR) AF: 0.882 AC: 36482 AN: 41362

American (AMR) AF: 0.823 AC: 12489 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3067 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4403 AN: 5138

South Asian (SAS) AF: 0.752 AC: 3617 AN: 4812

European-Finnish (FIN) AF: 0.816 AC: 8516 AN: 10440

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54741 AN: 67934

Other (OTH) AF: 0.844 AC: 1773 AN: 2100

Alfa AF: 0.761 Hom.: 2258

Bravo AF: 0.839

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.33
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1500038; hg19: chr12-59542155;