rs9332469

chr4-83916915-T-C

Variant summary

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

The ENST00000513489.5(LINC02994):n.401+18708A>G 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 0.338 in 152,080 control chromosomes in the GnomAD database, including 10,926 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 0.34 (10926 hom., cov: 32)
• Consequence: LINC02994 ENST00000513489.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02994	ENST00000513489.5	n.401+18708A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51454 AN: 151962 Hom.: 10919 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.338 AC: 51458 AN: 152080 Hom.: 10926 Cov.: 32 AF XY: 0.332 AC XY: 24676 AN XY: 74350

Gnomad4 AFR AF: 0.0935

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.356

Alfa AF: 0.401 Hom.: 2312

Bravo AF: 0.328

Asia WGS AF: 0.182 AC: 632 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332469; hg19: chr4-84838068;