12-59079191-T-C

Variant names:

• chr12-59079191-T-C
• rs2371978
• ENST00000716008.1:n.512+23083T>C

Variant summary

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

The ENST00000716008.1(LRIG3-DT):​n.512+23083T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,006 control chromosomes in the GnomAD database, including 44,095 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 0.75 (44095 hom., cov: 30)
• Consequence: LRIG3-DT ENST00000716008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRIG3-DT	NR_183518.1	n.264+23083T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRIG3-DT	ENST00000716008.1	n.512+23083T>C		intron_variant	Intron 3 of 5
LRIG3-DT	ENST00000716009.1	n.553+15116T>C		intron_variant	Intron 6 of 7
LRIG3-DT	ENST00000716010.1	n.326+23083T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113706 AN: 151888 Hom.: 44089 Cov.: 30

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.748 AC: 113731 AN: 152006 Hom.: 44095 Cov.: 30 AF XY: 0.750 AC XY: 55739 AN XY: 74300

African (AFR) AF: 0.552 AC: 22874 AN: 41406

American (AMR) AF: 0.662 AC: 10095 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2550 AN: 3470

East Asian (EAS) AF: 0.895 AC: 4601 AN: 5140

South Asian (SAS) AF: 0.823 AC: 3962 AN: 4812

European-Finnish (FIN) AF: 0.919 AC: 9754 AN: 10610

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.844 AC: 57368 AN: 68002

Other (OTH) AF: 0.707 AC: 1493 AN: 2112

Alfa AF: 0.805 Hom.: 209483

Bravo AF: 0.719

Asia WGS AF: 0.790 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2371978; hg19: chr12-59472972;