rs9293162

Variant names:

• chr5-25065361-C-T
• rs9293162
• ENST00000726616.1:n.446-16416G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000726616.1(LINC02228):​n.446-16416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0413 in 152,144 control chromosomes in the GnomAD database, including 151 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 0.041 (151 hom., cov: 33)
• Consequence: LINC02228 ENST00000726616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.960
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0413 (6288/152144) while in subpopulation AFR AF = 0.05 (2078/41534). AF 95% confidence interval is 0.0482. There are 151 homozygotes in GnomAd4. There are 2995 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 151 gene

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
LINC02228	ENST00000726616.1	n.446-16416G>A		intron_variant	Intron 4 of 4
LINC02228	ENST00000726617.1	n.350-16416G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6294 AN: 152026 Hom.: 153 Cov.: 33

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0413 AC: 6288 AN: 152144 Hom.: 151 Cov.: 33 AF XY: 0.0403 AC XY: 2995 AN XY: 74370

African (AFR) AF: 0.0500 AC: 2078 AN: 41534

American (AMR) AF: 0.0277 AC: 423 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3468

East Asian (EAS) AF: 0.0232 AC: 120 AN: 5174

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4814

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10586

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0415 AC: 2822 AN: 67968

Other (OTH) AF: 0.0469 AC: 99 AN: 2112

Alfa AF: 0.0437 Hom.: 437

Bravo AF: 0.0434

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.54
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs9293162; hg19: chr5-25065470;