15-26422218-G-A

Position:

• chr15-26422218-G-A

Variant summary

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

The ENST00000658140.1(LINC02248):​n.209-24211G>A 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 0.494 in 151,970 control chromosomes in the GnomAD database, including 19,432 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 0.49 (19432 hom., cov: 32)
• Consequence: LINC02248 ENST00000658140.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

LINC02248 (HGNC:53147): (long intergenic non-protein coding RNA 2248)

(HGNC:):

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 = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02248	XR_001751453.2	n.189-24211G>A		intron_variant, non_coding_transcript_variant
LOC105370740	XR_007064792.1	n.918-17952C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02248	ENST00000658140.1	n.209-24211G>A		intron_variant, non_coding_transcript_variant
	ENST00000660088.1	n.620-17952C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75044 AN: 151852 Hom.: 19401 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.494 AC: 75124 AN: 151970 Hom.: 19432 Cov.: 32 AF XY: 0.494 AC XY: 36720 AN XY: 74276

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.493

Alfa AF: 0.446 Hom.: 19603

Bravo AF: 0.499

Asia WGS AF: 0.364 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4906879; hg19: chr15-26667365;