chr2-65564447-C-T

Variant names:

• chr2-65564447-C-T
• rs897876
• ENST00000377977.3:n.862+63300C>T

Variant summary

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

The ENST00000377977.3(LINC02934):​n.862+63300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,118 control chromosomes in the GnomAD database, including 7,060 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 0.30 (7060 hom., cov: 32)
• Consequence: LINC02934 ENST00000377977.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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.862+63300C>T		intron_variant	Intron 4 of 4	2
LINC02934	ENST00000606978.5	n.455+81295C>T		intron_variant	Intron 4 of 9	5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45763 AN: 152000 Hom.: 7056 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.301 AC: 45788 AN: 152118 Hom.: 7060 Cov.: 32 AF XY: 0.301 AC XY: 22384 AN XY: 74354

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.304

Alfa AF: 0.304 Hom.: 14567

Bravo AF: 0.292

Asia WGS AF: 0.255 AC: 886 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	1.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs897876; hg19: chr2-65791581;