chr1-165478920-T-C

Position:

• chr1-165478920-T-C

Variant summary

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

The NR_026744.2(LRRC52-AS1):​n.1530-1805A>G 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 0.377 in 151,812 control chromosomes in the GnomAD database, including 11,723 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 0.38 (11723 hom., cov: 30)
• Consequence: LRRC52-AS1 NR_026744.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC52-AS1	NR_026744.2	n.1530-1805A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC52-AS1	ENST00000416424.5	n.1443-1805A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57213 AN: 151694 Hom.: 11728 Cov.: 30

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.377 AC: 57232 AN: 151812 Hom.: 11723 Cov.: 30 AF XY: 0.379 AC XY: 28080 AN XY: 74184

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.408

Alfa AF: 0.403 Hom.: 24305

Bravo AF: 0.384

Asia WGS AF: 0.613 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10918196; hg19: chr1-165448157;