rs2371978

Positions:

• chr12-59079191-T-C

Variant summary

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

The NR_183518.1(LRIG3-DT):​n.264+23083T>C variant causes a intron, non coding transcript 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 NR_183518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

LRIG3-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LRIG3-DT	NR_183518.1	n.264+23083T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.707

Alfa AF: 0.812 Hom.: 102596

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2371978; hg19: chr12-59472972;