rs2419914

Variant names:

• chr5-158417878-G-A
• rs2419914
• ENST00000809484.1:n.174-24641C>T

Variant summary

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

The ENST00000809484.1(LINC02227):​n.174-24641C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,894 control chromosomes in the GnomAD database, including 18,272 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 0.48 (18272 hom., cov: 32)
• Consequence: LINC02227 ENST00000809484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 4 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 = 0.597 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
LINC02227	ENST00000809484.1	n.174-24641C>T		intron_variant	Intron 2 of 3
LINC02227	ENST00000809485.1	n.213+12296C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72918 AN: 151776 Hom.: 18234 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.481 AC: 73006 AN: 151894 Hom.: 18272 Cov.: 32 AF XY: 0.475 AC XY: 35245 AN XY: 74236

African (AFR) AF: 0.603 AC: 24993 AN: 41462

American (AMR) AF: 0.382 AC: 5819 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1972 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1276 AN: 5136

South Asian (SAS) AF: 0.471 AC: 2272 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4039 AN: 10554

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

European-Non Finnish (NFE) AF: 0.457 AC: 31012 AN: 67904

Other (OTH) AF: 0.512 AC: 1077 AN: 2104

Alfa AF: 0.467 Hom.: 2135

Bravo AF: 0.480

Asia WGS AF: 0.419 AC: 1450 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	0.25
DANN	Benign	0.48
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2419914; hg19: chr5-157844886;