rs11134290

Variant names:

• chr5-8202423-C-T
• rs11134290
• ENST00000847314.1:n.456-9330G>A

Variant summary

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

The ENST00000847314.1(LINC02226):​n.456-9330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,204 control chromosomes in the GnomAD database, including 2,139 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 0.14 (2139 hom., cov: 32)
• Consequence: LINC02226 ENST00000847314.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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	ENST00000847314.1	n.456-9330G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21528 AN: 152086 Hom.: 2128 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.142 AC: 21577 AN: 152204 Hom.: 2139 Cov.: 32 AF XY: 0.136 AC XY: 10142 AN XY: 74418

African (AFR) AF: 0.282 AC: 11722 AN: 41512

American (AMR) AF: 0.106 AC: 1620 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 346 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5176

South Asian (SAS) AF: 0.0494 AC: 238 AN: 4822

European-Finnish (FIN) AF: 0.0501 AC: 532 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0991 AC: 6737 AN: 68004

Other (OTH) AF: 0.140 AC: 296 AN: 2110

Alfa AF: 0.112 Hom.: 487

Bravo AF: 0.153

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.27
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs11134290; hg19: chr5-8202536;