chr2-65663178-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377977.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02934	ENST00000377977.3	TSL:2	n.863-28604T>C		intron	N/A
	LINC02934	ENST00000606978.5	TSL:5	n.456-28604T>C		intron	N/A
	LINC02934	ENST00000822260.1		n.368-28604T>C		intron	N/A

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

African (AFR) AF: 0.414 AC: 17140 AN: 41440

American (AMR) AF: 0.335 AC: 5117 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3470

East Asian (EAS) AF: 0.147 AC: 760 AN: 5182

South Asian (SAS) AF: 0.219 AC: 1058 AN: 4824

European-Finnish (FIN) AF: 0.443 AC: 4672 AN: 10554

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31977 AN: 67958

Other (OTH) AF: 0.423 AC: 895 AN: 2114

Alfa AF: 0.392 Hom.: 4183

Bravo AF: 0.413

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	19
DANN	Benign	0.88
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs840777; hg19: chr2-65890312;