rs2419912

Variant names:

• chr5-158417527-T-C
• rs2419912
• ENST00000809484.1:n.174-24290A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-158417527-T-C
• chr5-158417527-T-G

Variant summary

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

The ENST00000809484.1(LINC02227):​n.174-24290A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,976 control chromosomes in the GnomAD database, including 17,465 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 0.47 (17465 hom., cov: 32)
• Consequence: LINC02227 ENST00000809484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 6 publications found

Genes affected

LINC02227 (HGNC:53096): (long intergenic non-protein coding RNA 2227)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809484.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02227	ENST00000809484.1		n.174-24290A>G		intron	N/A
	LINC02227	ENST00000809485.1		n.213+12647A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71552 AN: 151858 Hom.: 17435 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.471 AC: 71630 AN: 151976 Hom.: 17465 Cov.: 32 AF XY: 0.465 AC XY: 34528 AN XY: 74250

African (AFR) AF: 0.572 AC: 23737 AN: 41474

American (AMR) AF: 0.377 AC: 5755 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1971 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1272 AN: 5154

South Asian (SAS) AF: 0.471 AC: 2273 AN: 4828

European-Finnish (FIN) AF: 0.380 AC: 4015 AN: 10552

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31000 AN: 67940

Other (OTH) AF: 0.502 AC: 1059 AN: 2110

Alfa AF: 0.462 Hom.: 2095

Bravo AF: 0.470

Asia WGS AF: 0.414 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.32
PhyloP100		-0.78

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2419912;

hg19: chr5-157844535;