chr5-8212002-T-G

Variant names:

• chr5-8212002-T-G
• rs6893114
• ENST00000654773.1:n.262-2158A>C

Variant summary

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

The ENST00000654773.1(LINC02226):​n.262-2158A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 151,962 control chromosomes in the GnomAD database, including 49,532 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 0.80 (49532 hom., cov: 30)
• Consequence: LINC02226 ENST00000654773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 3 publications found

Genes affected

LINC02226 (HGNC:53095): (long intergenic non-protein coding RNA 2226)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.866 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
LINC02226	ENST00000654773.1	n.262-2158A>C		intron_variant	Intron 1 of 1
LINC02226	ENST00000847314.1	n.456-18909A>C		intron_variant	Intron 4 of 4
LINC02226	ENST00000847315.1	n.359-2158A>C		intron_variant	Intron 3 of 3
LINC02226	ENST00000847680.1	n.100-2158A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121645 AN: 151844 Hom.: 49508 Cov.: 30

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.801 AC: 121715 AN: 151962 Hom.: 49532 Cov.: 30 AF XY: 0.797 AC XY: 59220 AN XY: 74262

African (AFR) AF: 0.713 AC: 29507 AN: 41376

American (AMR) AF: 0.760 AC: 11597 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3074 AN: 3472

East Asian (EAS) AF: 0.530 AC: 2728 AN: 5152

South Asian (SAS) AF: 0.665 AC: 3194 AN: 4806

European-Finnish (FIN) AF: 0.909 AC: 9624 AN: 10588

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.872 AC: 59274 AN: 67996

Other (OTH) AF: 0.789 AC: 1664 AN: 2110

Alfa AF: 0.828 Hom.: 14683

Bravo AF: 0.786

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.70
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6893114; hg19: chr5-8212115;