4-83981811-C-T

Variant names:

• chr4-83981811-C-T
• rs9999681
• ENST00000513489.5:n.293+30244G>A

Variant summary

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

The ENST00000513489.5(LINC02994):​n.293+30244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,856 control chromosomes in the GnomAD database, including 2,537 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 0.18 (2537 hom., cov: 32)
• Consequence: LINC02994 ENST00000513489.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 5 publications found

Genes affected

LINC02994 (HGNC:56109): (long intergenic non-protein coding RNA 2994)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513489.5. 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
	LINC02994	NR_125909.1		n.810-11701G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02994	ENST00000513489.5	TSL:1	n.293+30244G>A		intron	N/A
	LINC02994	ENST00000508406.1	TSL:5	n.767-11701G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26687 AN: 151738 Hom.: 2523 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.176 AC: 26742 AN: 151856 Hom.: 2537 Cov.: 32 AF XY: 0.174 AC XY: 12920 AN XY: 74178

African (AFR) AF: 0.235 AC: 9733 AN: 41396

American (AMR) AF: 0.140 AC: 2143 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3472

East Asian (EAS) AF: 0.127 AC: 655 AN: 5154

South Asian (SAS) AF: 0.0989 AC: 476 AN: 4812

European-Finnish (FIN) AF: 0.129 AC: 1348 AN: 10480

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10857 AN: 67974

Other (OTH) AF: 0.185 AC: 389 AN: 2108

Alfa AF: 0.165 Hom.: 4118

Bravo AF: 0.181

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.013
DANN	Benign	0.61
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs9999681; hg19: chr4-84902964;