rs1426891

Variant names:

• chr15-26472746-G-A
• rs1426891
• ENST00000660088.2:n.426-1649C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660088.2(ENSG00000287280):​n.426-1649C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,762 control chromosomes in the GnomAD database, including 9,093 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 0.28 (9093 hom., cov: 32)
• Consequence: ENSG00000287280 ENST00000660088.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 3 publications found

Genes affected

ENSG00000287280 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660088.2. 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
	ENSG00000287280	ENST00000660088.2		n.426-1649C>T		intron	N/A
	ENSG00000287280	ENST00000826682.1		n.391-1649C>T		intron	N/A
	ENSG00000287280	ENST00000826683.1		n.426-1851C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42828 AN: 151644 Hom.: 9071 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.283 AC: 42889 AN: 151762 Hom.: 9093 Cov.: 32 AF XY: 0.279 AC XY: 20656 AN XY: 74142

African (AFR) AF: 0.601 AC: 24816 AN: 41282

American (AMR) AF: 0.230 AC: 3509 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3468

East Asian (EAS) AF: 0.151 AC: 782 AN: 5162

South Asian (SAS) AF: 0.183 AC: 885 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1583 AN: 10526

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9425 AN: 67930

Other (OTH) AF: 0.281 AC: 590 AN: 2102

Alfa AF: 0.148 Hom.: 1145

Bravo AF: 0.305

Asia WGS AF: 0.211 AC: 737 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.52
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1426891;

hg19: chr15-26717893;