rs4693646

Positions:

• chr4-83800661-A-G

Variant summary

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

The ENST00000513489.5(LINC02994):​n.559-4045T>C 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 0.439 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

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

LOC105377315 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377315	XR_938946.3	n.80+2088T>C		intron_variant, non_coding_transcript_variant
LOC105377315	XR_007058455.1	n.360+2088T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02994	ENST00000513489.5	n.559-4045T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.425

Alfa AF: 0.523 Hom.: 35424

Bravo AF: 0.421

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4693646; hg19: chr4-84721814;