12-59041249-T-C

Variant names:

• chr12-59041249-T-C
• rs1878871
• ENST00000804583.1:n.160T>C

Variant summary

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

The ENST00000804583.1(LRIG3-DT):​n.160T>C variant causes a non coding transcript exon 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 ENST00000804583.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 0 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=-0.83).
• 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 rank	MANE	Protein	UniProt
LRIG3-DT	NR_183518.1	n.162-14757T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRIG3-DT	ENST00000804583.1	n.160T>C		non_coding_transcript_exon_variant	Exon 1 of 5
LRIG3-DT	ENST00000547590.2	n.239-14757T>C		intron_variant	Intron 2 of 3	4
LRIG3-DT	ENST00000686887.2	n.248-14757T>C		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.190 AC: 7899 AN: 41516

American (AMR) AF: 0.0998 AC: 1525 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3472

East Asian (EAS) AF: 0.0324 AC: 168 AN: 5180

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4820

European-Finnish (FIN) AF: 0.0221 AC: 235 AN: 10612

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0260 AC: 1765 AN: 68010

Other (OTH) AF: 0.0866 AC: 183 AN: 2112

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
PhyloP100		0.33
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: rs1878871; hg19: chr12-59435030;