4-83916915-T-C

Variant names:

• chr4-83916915-T-C
• rs9332469
• ENST00000513489.5:n.401+18708A>G

Variant summary

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

The ENST00000513489.5(LINC02994):​n.401+18708A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 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=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02994	ENST00000513489.5	n.401+18708A>G		intron_variant	Intron 4 of 5	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

African (AFR) AF: 0.0935 AC: 3883 AN: 41528

American (AMR) AF: 0.413 AC: 6316 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1088 AN: 3472

East Asian (EAS) AF: 0.139 AC: 720 AN: 5172

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4822

European-Finnish (FIN) AF: 0.408 AC: 4306 AN: 10558

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32577 AN: 67934

Other (OTH) AF: 0.356 AC: 752 AN: 2110

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9332469; hg19: chr4-84838068;