14-82704378-A-T

Position:

• chr14-82704378-A-T

Variant summary

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

The NR_146650.1(LINC02301):​n.304-2323A>T 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 0.113 in 152,038 control chromosomes in the GnomAD database, including 1,255 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 0.11 (1255 hom., cov: 32)
• Consequence: LINC02301 NR_146650.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

Genes affected

LINC02301 (HGNC:53220): (long intergenic non-protein coding RNA 2301)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02301	NR_146650.1	n.304-2323A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02301	ENST00000662642.1	n.184+17009A>T		intron_variant, non_coding_transcript_variant
LINC02301	ENST00000555150.5	n.304-2323A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17149 AN: 151920 Hom.: 1253 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.113 AC: 17161 AN: 152038 Hom.: 1255 Cov.: 32 AF XY: 0.118 AC XY: 8750 AN XY: 74288

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0854

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0886 Hom.: 89

Bravo AF: 0.118

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2150333; hg19: chr14-83170722;