rs4693646

Variant names:

• chr4-83800661-A-G
• rs4693646
• ENST00000513489.5:n.559-4045T>C

Variant summary

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

The ENST00000513489.5(LINC02994):​n.559-4045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,994 control chromosomes in the GnomAD database, including 17,229 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 0.44 (17229 hom., cov: 32)
• Consequence: LINC02994 ENST00000513489.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 7 publications found

Genes affected

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

LOC105377315 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02994	ENST00000513489.5	TSL:1	n.559-4045T>C		intron	N/A
	LINC02994	ENST00000827819.1		n.92+2088T>C		intron	N/A
	LINC02994	ENST00000827820.1		n.81+2088T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66739 AN: 151876 Hom.: 17222 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.439 AC: 66760 AN: 151994 Hom.: 17229 Cov.: 32 AF XY: 0.444 AC XY: 32975 AN XY: 74272

African (AFR) AF: 0.149 AC: 6180 AN: 41476

American (AMR) AF: 0.492 AC: 7495 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3468

East Asian (EAS) AF: 0.730 AC: 3776 AN: 5172

South Asian (SAS) AF: 0.658 AC: 3172 AN: 4820

European-Finnish (FIN) AF: 0.532 AC: 5603 AN: 10540

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37539 AN: 67958

Other (OTH) AF: 0.425 AC: 896 AN: 2110

Alfa AF: 0.503 Hom.: 56527

Bravo AF: 0.421

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4693646; hg19: chr4-84721814;