rs166949

Variant names:

• chr1-165541053-G-A
• rs166949
• ENST00000416424.5:n.873-17966C>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.873-17966C>T variant causes a intron 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 ENST00000416424.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656
• 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=-0.82).
• 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 rank	MANE	Protein	UniProt
LRRC52-AS1	NR_026744.2	n.960-17966C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC52-AS1	ENST00000416424.5	n.873-17966C>T		intron_variant	Intron 2 of 5	1
LRRC52-AS1	ENST00000438275.5	n.933-12171C>T		intron_variant	Intron 3 of 7	1
LRRC52-AS1	ENST00000421273.5	n.909-17966C>T		intron_variant	Intron 3 of 6	2

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

African (AFR) AF: 0.828 AC: 34342 AN: 41486

American (AMR) AF: 0.957 AC: 14639 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3378 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.952 AC: 4592 AN: 4824

European-Finnish (FIN) AF: 0.992 AC: 10536 AN: 10622

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65690 AN: 68016

Other (OTH) AF: 0.937 AC: 1981 AN: 2114

Alfa AF: 0.939 Hom.: 10672

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
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs166949; hg19: chr1-165510290;