chr14-53781365-C-T

Position:

• chr14-53781365-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.343+11977G>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 0.211 in 151,892 control chromosomes in the GnomAD database, including 3,535 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 0.21 (3535 hom., cov: 32)
• Consequence: LINC02331 NR_184221.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02331	NR_184221.1	n.343+11977G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02331	ENST00000418927.2	n.580+11889G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000648066.1	n.792-3780C>T		intron_variant, non_coding_transcript_variant
	ENST00000649040.1	n.65+15646C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32052 AN: 151772 Hom.: 3533 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.211 AC: 32070 AN: 151892 Hom.: 3535 Cov.: 32 AF XY: 0.219 AC XY: 16279 AN XY: 74190

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.206

Alfa AF: 0.197 Hom.: 4293

Bravo AF: 0.202

Asia WGS AF: 0.324 AC: 1120 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17126895; hg19: chr14-54248083;