rs17008416

Variant names:

• chr4-84253523-G-A
• rs17008416
• ENST00000513489.5:n.123-10307C>T

Variant summary

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

The ENST00000513489.5(LINC02994):​n.123-10307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 152,084 control chromosomes in the GnomAD database, including 367 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 0.063 (367 hom., cov: 32)
• Consequence: LINC02994 ENST00000513489.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02994	NR_125909.1		n.517-10307C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02994	ENST00000513489.5	TSL:1	n.123-10307C>T		intron	N/A
	LINC02994	ENST00000508406.1	TSL:5	n.474-10307C>T		intron	N/A
	LINC02994	ENST00000657959.1		n.50-10307C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9581 AN: 151966 Hom.: 368 Cov.: 32

Gnomad AFR AF: 0.0593

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0392

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0630 AC: 9580 AN: 152084 Hom.: 367 Cov.: 32 AF XY: 0.0630 AC XY: 4687 AN XY: 74364

African (AFR) AF: 0.0593 AC: 2462 AN: 41520

American (AMR) AF: 0.0660 AC: 1007 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3472

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5182

South Asian (SAS) AF: 0.133 AC: 642 AN: 4814

European-Finnish (FIN) AF: 0.0392 AC: 415 AN: 10590

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0674 AC: 4579 AN: 67920

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0706 Hom.: 657

Bravo AF: 0.0631

Asia WGS AF: 0.0800 AC: 278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.41
PhyloP100		-0.0070
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17008416;

hg19: chr4-85174676;