rs1025356

Variant names:

• chr15-30292060-A-G
• rs1025356
• ENST00000749194.1:n.394-30299A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000749194.1(LINC02249):​n.394-30299A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 11)
  • Failed GnomAD Quality Control
• Consequence: LINC02249 ENST00000749194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 1 publications found

Genes affected

LINC02249 (HGNC:32351): (long intergenic non-protein coding RNA 2249)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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
LINC02249	ENST00000749194.1	n.394-30299A>G		intron_variant	Intron 2 of 8
LINC02249	ENST00000749195.1	n.257-30299A>G		intron_variant	Intron 2 of 9
LINC02249	ENST00000749196.1	n.222-30299A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 88268 Hom.: 0 Cov.: 11

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 88268 Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0 AN XY: 42336

African (AFR) AF: 0.00 AC: 0 AN: 21914

American (AMR) AF: 0.00 AC: 0 AN: 8722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2188

East Asian (EAS) AF: 0.00 AC: 0 AN: 4340

South Asian (SAS) AF: 0.00 AC: 0 AN: 2552

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4698

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 178

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 41970

Other (OTH) AF: 0.00 AC: 0 AN: 1116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.84
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs1025356; hg19: chr15-30584263;