rs17121944

chr12-59046451-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.162-9555T>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 0.0491 in 152,234 control chromosomes in the GnomAD database, including 282 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 0.049 (282 hom., cov: 32)
• Consequence: LRIG3-DT NR_183518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRIG3-DT	NR_183518.1	n.162-9555T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRIG3-DT	ENST00000686887.1	n.232-9555T>C		intron_variant, non_coding_transcript_variant
LRIG3-DT	ENST00000547590.1	n.227-9555T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7450 AN: 152116 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0226

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0491 AC: 7469 AN: 152234 Hom.: 282 Cov.: 32 AF XY: 0.0475 AC XY: 3540 AN XY: 74450

Gnomad4 AFR AF: 0.0964

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.0321

Gnomad4 SAS AF: 0.0118

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0226

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0262 Hom.: 192

Bravo AF: 0.0562

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17121944; hg19: chr12-59440232;