rs11584700

Variant names:

• chr1-204607855-A-G
• rs11584700
• XR_007066819.1:n.2612A>G

Variant summary

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

The XR_007066819.1(LRRN2-AS1):​n.2612A>G 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 0.171 in 152,098 control chromosomes in the GnomAD database, including 2,628 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 0.17 (2628 hom., cov: 32)
• Consequence: LRRN2-AS1 XR_007066819.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 25 publications found

Genes affected

LRRN2-AS1 (HGNC:58404):

ENSG00000240710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453895.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000240710	ENST00000453895.1	TSL:3	n.117+4704A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26011 AN: 151980 Hom.: 2632 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.171 AC: 26001 AN: 152098 Hom.: 2628 Cov.: 32 AF XY: 0.172 AC XY: 12758 AN XY: 74324

African (AFR) AF: 0.0772 AC: 3203 AN: 41516

American (AMR) AF: 0.114 AC: 1740 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1640 AN: 5148

South Asian (SAS) AF: 0.249 AC: 1197 AN: 4812

European-Finnish (FIN) AF: 0.223 AC: 2354 AN: 10568

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14626 AN: 67976

Other (OTH) AF: 0.164 AC: 347 AN: 2110

Alfa AF: 0.196 Hom.: 4804

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.1
DANN	Benign	0.82
PhyloP100		-0.95

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11584700;

hg19: chr1-204576983;