rs16860281

Variant names:

• chr3-148277560-T-C
• rs16860281
• ENST00000733403.1:n.355A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000733403.1(LINC02045):​n.355A>G variant causes a non coding transcript exon 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 ENST00000733403.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02045	ENST00000733403.1	n.355A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02045	ENST00000460324.3	n.305+2222A>G		intron_variant	Intron 1 of 3	3
LINC02045	ENST00000662134.1	n.317+2222A>G		intron_variant	Intron 1 of 5

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

African (AFR) AF: 0.207 AC: 8578 AN: 41524

American (AMR) AF: 0.0694 AC: 1061 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0365 AC: 176 AN: 4828

European-Finnish (FIN) AF: 0.0586 AC: 622 AN: 10618

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0856 AC: 5825 AN: 68024

Other (OTH) AF: 0.0889 AC: 188 AN: 2114

Alfa AF: 0.0952 Hom.: 2197

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
PhyloP100		0.85
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16860281; hg19: chr3-147995347;