chr1-165496044-G-A

Variant names:

• chr1-165496044-G-A
• rs4657449
• ENST00000416424.5:n.1183+5387C>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.1183+5387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,198 control chromosomes in the GnomAD database, including 4,075 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 0.16 (4075 hom., cov: 33)
• Consequence: LRRC52-AS1 ENST00000416424.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 13 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC52-AS1	NR_026744.2	n.1270+5387C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC52-AS1	ENST00000416424.5	n.1183+5387C>T		intron_variant	Intron 4 of 5	1
LRRC52-AS1	ENST00000438275.5	n.1445+2968C>T		intron_variant	Intron 7 of 7	1
LRRC52-AS1	ENST00000452283.5	n.731-2841C>T		intron_variant	Intron 5 of 5	1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24315 AN: 152080 Hom.: 4051 Cov.: 33

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.160 AC: 24378 AN: 152198 Hom.: 4075 Cov.: 33 AF XY: 0.174 AC XY: 12922 AN XY: 74404

African (AFR) AF: 0.100 AC: 4164 AN: 41502

American (AMR) AF: 0.320 AC: 4899 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 340 AN: 3472

East Asian (EAS) AF: 0.864 AC: 4476 AN: 5182

South Asian (SAS) AF: 0.455 AC: 2193 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1431 AN: 10582

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6416 AN: 68022

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.134 Hom.: 12868

Bravo AF: 0.171

Asia WGS AF: 0.639 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4657449; hg19: chr1-165465281;