2-219714550-A-T

Position:

• chr2-219714550-A-T

Variant summary

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

The ENST00000606673.1(LINC02832):​n.119-22904A>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 0.102 in 153,584 control chromosomes in the GnomAD database, including 1,004 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 0.10 (989 hom., cov: 33)
  • Exomes 𝑓: 0.13 (15 hom.)
• Consequence: LINC02832 ENST00000606673.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

LINC02832 (HGNC:54366): (long intergenic non-protein coding RNA 2832)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02832	ENST00000606673.1	n.119-22904A>T		intron_variant, non_coding_transcript_variant		3
LINC02832	ENST00000416861.1	n.360A>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15562 AN: 152186 Hom.: 990 Cov.: 33

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0428

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0638

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.134

GnomAD4 exome AF: 0.134 AC: 172 AN: 1280 Hom.: 15 Cov.: 0 AF XY: 0.141 AC XY: 111 AN XY: 790

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0625

Gnomad4 SAS exome AF: 0.136

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.102 AC: 15553 AN: 152304 Hom.: 989 Cov.: 33 AF XY: 0.0993 AC XY: 7397 AN XY: 74484

Gnomad4 AFR AF: 0.0350

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0427

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0638

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0520 Hom.: 45

Bravo AF: 0.103

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714132; hg19: chr2-220579272;