ENST00000416424.5:n.986+1426C>T

Variant names:

• chr1-165521548-G-A
• rs285470
• ENST00000416424.5:n.986+1426C>T

Variant summary

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

The ENST00000416424.5(LRRC52-AS1):​n.986+1426C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,228 control chromosomes in the GnomAD database, including 58,052 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 0.87 (58052 hom., cov: 33)
• Consequence: LRRC52-AS1 ENST00000416424.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 5 publications found

Genes affected

LRRC52-AS1 (HGNC:54044): (LRRC52 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC52-AS1	NR_026744.2	n.1073+1426C>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC52-AS1	ENST00000416424.5	n.986+1426C>T		intron_variant	Intron 3 of 5	1
LRRC52-AS1	ENST00000438275.5	n.1146+1426C>T		intron_variant	Intron 5 of 7	1
LRRC52-AS1	ENST00000452283.5	n.179-12745C>T		intron_variant	Intron 1 of 5	1

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132588 AN: 152110 Hom.: 58008 Cov.: 33

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.872 AC: 132689 AN: 152228 Hom.: 58052 Cov.: 33 AF XY: 0.872 AC XY: 64874 AN XY: 74422

African (AFR) AF: 0.782 AC: 32454 AN: 41516

American (AMR) AF: 0.927 AC: 14182 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3242 AN: 3468

East Asian (EAS) AF: 0.935 AC: 4845 AN: 5184

South Asian (SAS) AF: 0.864 AC: 4170 AN: 4826

European-Finnish (FIN) AF: 0.888 AC: 9405 AN: 10596

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61475 AN: 68028

Other (OTH) AF: 0.893 AC: 1886 AN: 2112

Alfa AF: 0.889 Hom.: 27443

Bravo AF: 0.872

Asia WGS AF: 0.891 AC: 3100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.27
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs285470; hg19: chr1-165490785;