rs1381281

Variant names:

• chr14-98149434-T-C
• rs1381281
• ENST00000555776.1:n.121+55589A>G

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.121+55589A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,132 control chromosomes in the GnomAD database, including 9,720 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 0.35 (9720 hom., cov: 33)
• Consequence: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 3 publications found

Genes affected

ENSG00000259097 (HGNC:):

LINC02295 (HGNC:53211): (long intergenic non-protein coding RNA 2295)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555776.1. 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
	LINC02295	NR_184268.1		n.529+10124T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259097	ENST00000555776.1	TSL:4	n.121+55589A>G		intron	N/A
	LINC02295	ENST00000684820.2		n.529+10124T>C		intron	N/A
	LINC02295	ENST00000691452.2		n.423-13012T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53389 AN: 152014 Hom.: 9713 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.351 AC: 53430 AN: 152132 Hom.: 9720 Cov.: 33 AF XY: 0.345 AC XY: 25631 AN XY: 74370

African (AFR) AF: 0.300 AC: 12458 AN: 41486

American (AMR) AF: 0.330 AC: 5047 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3470

East Asian (EAS) AF: 0.172 AC: 893 AN: 5192

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4822

European-Finnish (FIN) AF: 0.329 AC: 3477 AN: 10572

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27386 AN: 67980

Other (OTH) AF: 0.378 AC: 800 AN: 2116

Alfa AF: 0.385 Hom.: 6044

Bravo AF: 0.350

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.45
PhyloP100		-0.85

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: rs1381281;

hg19: chr14-98615771;