1-204573452-T-C

Variant names:

• chr1-204573452-T-C
• rs12039454
• XR_007066816.1:n.2425T>C

Variant summary

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

The XR_007066816.1(LRRN2-AS1):​n.2425T>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 0.561 in 152,112 control chromosomes in the GnomAD database, including 26,602 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 0.56 (26602 hom., cov: 32)
• Consequence: LRRN2-AS1 XR_007066816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 12 publications found

Genes affected

LRRN2-AS1 (HGNC:58404):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRN2-AS1	XR_007066816.1	n.2425T>C		non_coding_transcript_exon_variant	Exon 1 of 12
LRRN2-AS1	XR_007066814.1	n.1204-235T>C		intron_variant	Intron 2 of 12
LRRN2-AS1	XR_007066815.1	n.131-235T>C		intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85263 AN: 151994 Hom.: 26601 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.561 AC: 85271 AN: 152112 Hom.: 26602 Cov.: 32 AF XY: 0.567 AC XY: 42190 AN XY: 74352

African (AFR) AF: 0.264 AC: 10969 AN: 41494

American (AMR) AF: 0.590 AC: 9024 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2105 AN: 3468

East Asian (EAS) AF: 0.680 AC: 3508 AN: 5162

South Asian (SAS) AF: 0.599 AC: 2881 AN: 4810

European-Finnish (FIN) AF: 0.795 AC: 8409 AN: 10584

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46333 AN: 67990

Other (OTH) AF: 0.565 AC: 1195 AN: 2114

Alfa AF: 0.655 Hom.: 15878

Bravo AF: 0.533

Asia WGS AF: 0.587 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.4
DANN	Benign	0.77
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12039454; hg19: chr1-204542580;