ENST00000787193.1:n.206C>T

Variant names:

• chr3-130201415-C-T
• rs2587988
• ENST00000787193.1:n.206C>T

Variant summary

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

The ENST00000787193.1(LINC02021):​n.206C>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 0.28 in 152,122 control chromosomes in the GnomAD database, including 6,803 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 0.28 (6803 hom., cov: 32)
• Consequence: LINC02021 ENST00000787193.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 4 publications found

Genes affected

LINC02021 (HGNC:52856): (long intergenic non-protein coding RNA 2021)

LOC124909433 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787193.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02021	ENST00000787193.1		n.206C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC02021	ENST00000787194.1		n.483C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC02021	ENST00000787195.1		n.912C>T		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42545 AN: 152004 Hom.: 6792 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.280 AC: 42570 AN: 152122 Hom.: 6803 Cov.: 32 AF XY: 0.286 AC XY: 21240 AN XY: 74346

African (AFR) AF: 0.144 AC: 5979 AN: 41534

American (AMR) AF: 0.420 AC: 6420 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1122 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2694 AN: 5164

South Asian (SAS) AF: 0.388 AC: 1867 AN: 4810

European-Finnish (FIN) AF: 0.290 AC: 3059 AN: 10562

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20403 AN: 67988

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.302 Hom.: 31913

Bravo AF: 0.285

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.24
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2587988; hg19: chr3-129920258;