rs2014790

chr5-25173090-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147006.1(LINC02228):n.211-5899A>G variant causes a intron, non coding transcript 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 NR_147006.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02228	NR_147006.1	n.211-5899A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02228	ENST00000641970.1	n.245-5899A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.166

Alfa AF: 0.164 Hom.: 250

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2014790; hg19: chr5-25173199;