chr5-25173090-T-C

Variant names:

• chr5-25173090-T-C
• rs2014790
• ENST00000507600.3:n.261-5899A>G

Variant summary

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

The ENST00000507600.3(LINC02228):​n.261-5899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,096 control chromosomes in the GnomAD database, including 2,060 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 0.16 (2060 hom., cov: 32)
• Consequence: LINC02228 ENST00000507600.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 2 publications found

Genes affected

LINC02228 (HGNC:53097): (long intergenic non-protein coding RNA 2228)

LINC02211 (HGNC:53078): (long intergenic non-protein coding RNA 2211)

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 = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02228	NR_147006.1	n.211-5899A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02228	ENST00000507600.3	n.261-5899A>G		intron_variant	Intron 1 of 4	2
LINC02228	ENST00000641261.2	n.511-5899A>G		intron_variant	Intron 1 of 4
LINC02228	ENST00000641970.2	n.263-5899A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24594 AN: 151978 Hom.: 2054 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.162 AC: 24632 AN: 152096 Hom.: 2060 Cov.: 32 AF XY: 0.158 AC XY: 11783 AN XY: 74352

African (AFR) AF: 0.226 AC: 9398 AN: 41494

American (AMR) AF: 0.108 AC: 1647 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3466

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5174

South Asian (SAS) AF: 0.138 AC: 667 AN: 4820

European-Finnish (FIN) AF: 0.156 AC: 1648 AN: 10578

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10007 AN: 67976

Other (OTH) AF: 0.166 AC: 350 AN: 2110

Alfa AF: 0.167 Hom.: 268

Bravo AF: 0.159

Asia WGS AF: 0.128 AC: 445 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.71
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2014790; hg19: chr5-25173199;