chr2-65564447-C-T

Position:

• chr2-65564447-C-T

Variant summary

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

The ENST00000606978.5(LINC02934):​n.455+81295C>T 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 0.301 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 ENST00000606978.5 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5	n.455+81295C>T		intron_variant, non_coding_transcript_variant		5
LINC02934	ENST00000377977.3	n.862+63300C>T		intron_variant, non_coding_transcript_variant		2

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;