rs285424

chr1-165533954-A-Gchr1-165533954-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026744.2(LRRC52-AS1):n.960-10867T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,152 control chromosomes in the GnomAD database, including 66,019 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 0.93 (66019 hom., cov: 30)
• Consequence: LRRC52-AS1 NR_026744.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC52-AS1	NR_026744.2	n.960-10867T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC52-AS1	ENST00000416424.5	n.873-10867T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141281 AN: 152034 Hom.: 65971 Cov.: 30

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.929 AC: 141385 AN: 152152 Hom.: 66019 Cov.: 30 AF XY: 0.931 AC XY: 69285 AN XY: 74390

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.973

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.937

Alfa AF: 0.928 Hom.: 8887

Bravo AF: 0.922

Asia WGS AF: 0.960 AC: 3339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285424; hg19: chr1-165503191;