rs16860281

chr3-148277560-T-C

Variant summary

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

The ENST00000662134.1(LINC02045):n.317+2222A>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 0.11 in 152,272 control chromosomes in the GnomAD database, including 1,193 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 0.11 (1193 hom., cov: 32)
• Consequence: LINC02045 ENST00000662134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854

Genes affected

LINC02045 (HGNC:52885): (long intergenic non-protein coding RNA 2045)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02045	ENST00000662134.1	n.317+2222A>G		intron_variant, non_coding_transcript_variant
LINC02045	ENST00000460324.2	n.304+2222A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16710 AN: 152154 Hom.: 1189 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0856

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.110 AC: 16742 AN: 152272 Hom.: 1193 Cov.: 32 AF XY: 0.106 AC XY: 7867 AN XY: 74478

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0365

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0856

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0883 Hom.: 1083

Bravo AF: 0.116

Asia WGS AF: 0.0430 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16860281; hg19: chr3-147995347;