rs17741027

Variant names:

• chr14-87405491-A-G
• rs17741027
• ENST00000557070.1:n.329+889T>C

Variant summary

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

The ENST00000557070.1(LINC02296):​n.329+889T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,150 control chromosomes in the GnomAD database, including 124 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 0.039 (124 hom., cov: 32)
• Consequence: LINC02296 ENST00000557070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06
• Publications: 3 publications found

Genes affected

LINC02296 (HGNC:53212): (long intergenic non-protein coding RNA 2296)

ENSG00000310449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0391 (5955/152150) while in subpopulation EAS AF = 0.0497 (256/5154). AF 95% confidence interval is 0.0447. There are 124 homozygotes in GnomAd4. There are 2900 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 124 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557070.1. 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
	LINC02296	ENST00000557070.1	TSL:4	n.329+889T>C		intron	N/A
	LINC02296	ENST00000716942.1		n.527+889T>C		intron	N/A
	LINC02296	ENST00000716943.1		n.517+889T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5956 AN: 152032 Hom.: 124 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0254

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0391 AC: 5955 AN: 152150 Hom.: 124 Cov.: 32 AF XY: 0.0390 AC XY: 2900 AN XY: 74396

African (AFR) AF: 0.0359 AC: 1492 AN: 41508

American (AMR) AF: 0.0254 AC: 388 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 242 AN: 3470

East Asian (EAS) AF: 0.0497 AC: 256 AN: 5154

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4822

European-Finnish (FIN) AF: 0.0479 AC: 508 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0413 AC: 2808 AN: 67996

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

Alfa AF: 0.0404 Hom.: 406

Bravo AF: 0.0361

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.65
PhyloP100		2.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17741027; hg19: chr14-87871835;