rs10494443

Variant names:

• chr1-165511223-G-A
• rs10494443
• ENST00000416424.5:n.987-9596C>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.987-9596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0443 in 152,196 control chromosomes in the GnomAD database, including 221 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 0.044 (221 hom., cov: 32)
• Consequence: LRRC52-AS1 ENST00000416424.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 2 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416424.5. 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
	LRRC52-AS1	NR_026744.2		n.1074-9596C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC52-AS1	ENST00000416424.5	TSL:1	n.987-9596C>T		intron	N/A
	LRRC52-AS1	ENST00000438275.5	TSL:1	n.1147-9596C>T		intron	N/A
	LRRC52-AS1	ENST00000452283.5	TSL:1	n.179-2420C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6731 AN: 152078 Hom.: 221 Cov.: 32

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.00801

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0443 AC: 6741 AN: 152196 Hom.: 221 Cov.: 32 AF XY: 0.0424 AC XY: 3152 AN XY: 74408

African (AFR) AF: 0.0858 AC: 3562 AN: 41514

American (AMR) AF: 0.0355 AC: 543 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4810

European-Finnish (FIN) AF: 0.00801 AC: 85 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0334 AC: 2269 AN: 68012

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.0440 Hom.: 27

Bravo AF: 0.0488

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.55
DANN	Benign	0.87
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10494443; hg19: chr1-165480460;