rs17008416

chr4-84253523-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125909.1(LINC02994):n.517-10307C>T variant causes a intron, non coding transcript 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 NR_125909.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02994	NR_125909.1	n.517-10307C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02994	ENST00000513489.5	n.123-10307C>T		intron_variant, non_coding_transcript_variant		1
LINC02994	ENST00000508406.1	n.474-10307C>T		intron_variant, non_coding_transcript_variant		5
LINC02994	ENST00000657959.1	n.50-10307C>T		intron_variant, non_coding_transcript_variant
LINC02994	ENST00000668493.1	n.537-10307C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.0660

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0392

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0716 Hom.: 541

Bravo AF: 0.0631

Asia WGS AF: 0.0800 AC: 278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17008416; hg19: chr4-85174676;