chr12-59046451-T-C

Variant names:

• chr12-59046451-T-C
• rs17121944
• ENST00000547590.2:n.239-9555T>C

Variant summary

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

The ENST00000547590.2(LRIG3-DT):​n.239-9555T>C variant causes a intron 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 ENST00000547590.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547590.2. 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
	LRIG3-DT	NR_183518.1		n.162-9555T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRIG3-DT	ENST00000547590.2	TSL:4	n.239-9555T>C		intron	N/A
	LRIG3-DT	ENST00000686887.2		n.248-9555T>C		intron	N/A
	LRIG3-DT	ENST00000716008.1		n.410-9555T>C		intron	N/A

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

African (AFR) AF: 0.0964 AC: 4003 AN: 41544

American (AMR) AF: 0.0841 AC: 1286 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3466

East Asian (EAS) AF: 0.0321 AC: 166 AN: 5166

South Asian (SAS) AF: 0.0118 AC: 57 AN: 4828

European-Finnish (FIN) AF: 0.0219 AC: 232 AN: 10612

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0226 AC: 1535 AN: 68014

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0303 Hom.: 529

Bravo AF: 0.0562

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.68
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17121944; hg19: chr12-59440232;