ENST00000377977.3:n.863-28604T>C

Variant names:

• chr2-65663178-T-C
• rs840777
• ENST00000377977.3:n.863-28604T>C

Variant summary

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

The ENST00000377977.3(LINC02934):​n.863-28604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,030 control chromosomes in the GnomAD database, including 13,695 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 0.42 (13695 hom., cov: 32)
• Consequence: LINC02934 ENST00000377977.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

Genes affected

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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
LINC02934	ENST00000377977.3	n.863-28604T>C		intron_variant	Intron 4 of 4	2
LINC02934	ENST00000606978.5	n.456-28604T>C		intron_variant	Intron 4 of 9	5

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63599 AN: 151912 Hom.: 13689 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.419 AC: 63636 AN: 152030 Hom.: 13695 Cov.: 32 AF XY: 0.411 AC XY: 30553 AN XY: 74294

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.423

Alfa AF: 0.377 Hom.: 1919

Bravo AF: 0.413

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	19
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840777; hg19: chr2-65890312;