rs4657449

Positions:

• chr1-165496044-G-A
• chr1-165496044-G-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.1270+5387C>T 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 0.16 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 NR_026744.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

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=-0.88).
• 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/exons	MANE	UniProt
LRRC52-AS1	NR_026744.2	n.1270+5387C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC52-AS1	ENST00000416424.5	n.1183+5387C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.165

Alfa AF: 0.133 Hom.: 6650

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4657449; hg19: chr1-165465281;