ENST00000662083.1:n.46+28146A>C

Variant names:

• chr1-229155904-T-G
• rs9287024
• ENST00000662083.1:n.46+28146A>C

Variant summary

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

The ENST00000662083.1(LINC02814):​n.46+28146A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,136 control chromosomes in the GnomAD database, including 22,712 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 0.52 (22712 hom., cov: 32)
• Consequence: LINC02814 ENST00000662083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

Genes affected

LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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
LINC02814	ENST00000662083.1	n.46+28146A>C		intron_variant	Intron 1 of 4
LINC02814	ENST00000666388.1	n.337+41794A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79099 AN: 152018 Hom.: 22707 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.520 AC: 79120 AN: 152136 Hom.: 22712 Cov.: 32 AF XY: 0.520 AC XY: 38687 AN XY: 74374

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.559

Alfa AF: 0.602 Hom.: 29102

Bravo AF: 0.511

Asia WGS AF: 0.570 AC: 1985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287024; hg19: chr1-229291651;