rs17126951

chr14-53810072-C-T

Variant summary

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

The NR_184221.1(LINC02331):n.289-16676G>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 0.0839 in 152,036 control chromosomes in the GnomAD database, including 1,529 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 0.084 (1529 hom., cov: 32)
• Consequence: LINC02331 NR_184221.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

LINC02331 (HGNC:53251): (long intergenic non-protein coding RNA 2331)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02331	NR_184221.1	n.289-16676G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02331	ENST00000418927.2	n.438-16676G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000649040.1	n.65+44353C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12693 AN: 151918 Hom.: 1515 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.0207

Gnomad SAS AF: 0.0134

Gnomad FIN AF: 0.00255

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00920

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0839 AC: 12752 AN: 152036 Hom.: 1529 Cov.: 32 AF XY: 0.0817 AC XY: 6071 AN XY: 74326

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.00808

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.00255

Gnomad4 NFE AF: 0.00920

Gnomad4 OTH AF: 0.0644

Alfa AF: 0.0215 Hom.: 198

Bravo AF: 0.0946

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.9
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17126951; hg19: chr14-54276790;