1-229155904-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662083.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02814	ENST00000662083.1		n.46+28146A>C		intron	N/A
	LINC02814	ENST00000666388.1		n.337+41794A>C		intron	N/A
	LINC02814	ENST00000716797.1		n.183+28146A>C		intron	N/A

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

African (AFR) AF: 0.259 AC: 10729 AN: 41504

American (AMR) AF: 0.582 AC: 8898 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2424 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3688 AN: 5176

South Asian (SAS) AF: 0.547 AC: 2633 AN: 4814

European-Finnish (FIN) AF: 0.597 AC: 6305 AN: 10570

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42506 AN: 68002

Other (OTH) AF: 0.559 AC: 1181 AN: 2114

Alfa AF: 0.589 Hom.: 36210

Bravo AF: 0.511

Asia WGS AF: 0.570 AC: 1985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.35
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs9287024; hg19: chr1-229291651;