chr1-229059346-T-A

Variant names:

• chr1-229059346-T-A
• rs4654712
• ENST00000718074.1:n.466-21410A>T

Variant summary

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

The ENST00000718074.1(LINC02814):​n.466-21410A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,110 control chromosomes in the GnomAD database, including 25,603 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 0.58 (25603 hom., cov: 34)
• Consequence: LINC02814 ENST00000718074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718074.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02814	ENST00000718074.1		n.466-21410A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88001 AN: 151992 Hom.: 25574 Cov.: 34

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.579 AC: 88079 AN: 152110 Hom.: 25603 Cov.: 34 AF XY: 0.580 AC XY: 43165 AN XY: 74370

African (AFR) AF: 0.564 AC: 23393 AN: 41480

American (AMR) AF: 0.566 AC: 8647 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1876 AN: 3472

East Asian (EAS) AF: 0.575 AC: 2976 AN: 5178

South Asian (SAS) AF: 0.578 AC: 2794 AN: 4830

European-Finnish (FIN) AF: 0.588 AC: 6216 AN: 10568

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40306 AN: 67978

Other (OTH) AF: 0.549 AC: 1160 AN: 2112

Alfa AF: 0.591 Hom.: 3342

Bravo AF: 0.574

Asia WGS AF: 0.569 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.66
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4654712; hg19: chr1-229195093; COSMIC: COSV69481192;