rs1878871

chr12-59041249-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.162-14757T>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 0.0788 in 152,208 control chromosomes in the GnomAD database, including 882 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 0.079 (882 hom., cov: 33)
• Consequence: LRIG3-DT NR_183518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRIG3-DT	NR_183518.1	n.162-14757T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRIG3-DT	ENST00000686887.1	n.232-14757T>C		intron_variant, non_coding_transcript_variant
LRIG3-DT	ENST00000547590.1	n.227-14757T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11974 AN: 152090 Hom.: 878 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0788 AC: 11998 AN: 152208 Hom.: 882 Cov.: 33 AF XY: 0.0764 AC XY: 5684 AN XY: 74410

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0998

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.0324

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0260

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0614 Hom.: 96

Bravo AF: 0.0891

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.4
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878871; hg19: chr12-59435030;