rs166949

Positions:

• chr1-165541053-G-A

Variant summary

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

The NR_026744.2(LRRC52-AS1):​n.960-17966C>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 0.929 in 152,228 control chromosomes in the GnomAD database, including 66,070 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 (66070 hom., cov: 32)
• Consequence: LRRC52-AS1 NR_026744.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

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=-0.82).
• 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.960-17966C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC52-AS1	ENST00000416424.5	n.873-17966C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141374 AN: 152110 Hom.: 66022 Cov.: 32

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: 0.952

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.929 AC: 141478 AN: 152228 Hom.: 66070 Cov.: 32 AF XY: 0.931 AC XY: 69336 AN XY: 74440

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: 0.942 Hom.: 10405

Bravo AF: 0.922

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166949; hg19: chr1-165510290;