chr1-204573452-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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;