2-219714550-A-T

Variant names:

• chr2-219714550-A-T
• rs714132
• ENST00000416861.1:n.360A>T

Variant summary

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

The ENST00000416861.1(LINC02832):​n.360A>T variant causes a non coding transcript exon 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 ENST00000416861.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02832	ENST00000416861.1	n.360A>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC02832	ENST00000606673.1	n.119-22904A>T		intron_variant	Intron 1 of 1	3
LINC02832	ENST00000724275.1	n.100-22904A>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.00 AC: 0 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AF: 0.0625 AC: 2 AN: 32

South Asian (SAS) AF: 0.136 AC: 89 AN: 654

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.146 AC: 77 AN: 528

Other (OTH) AF: 0.143 AC: 4 AN: 28

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

African (AFR) AF: 0.0350 AC: 1456 AN: 41570

American (AMR) AF: 0.135 AC: 2064 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3468

East Asian (EAS) AF: 0.0427 AC: 221 AN: 5180

South Asian (SAS) AF: 0.148 AC: 714 AN: 4826

European-Finnish (FIN) AF: 0.0638 AC: 677 AN: 10610

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9378 AN: 68024

Other (OTH) AF: 0.132 AC: 279 AN: 2116

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs714132; hg19: chr2-220579272;