chr2-23378685-A-G

Variant names:

• chr2-23378685-A-G
• rs2577756
• ENST00000421563.5:n.80-1759T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421563.5(LINC02923):​n.80-1759T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,178 control chromosomes in the GnomAD database, including 39,882 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 0.71 (39882 hom., cov: 33)
• Consequence: LINC02923 ENST00000421563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 5 publications found

Genes affected

LINC02923 (HGNC:55672): (long intergenic non-protein coding RNA 2923)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421563.5. 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
	LINC02923	NR_187213.1		n.6099-1759T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02923	ENST00000421563.5	TSL:4	n.80-1759T>C		intron	N/A
	LINC02923	ENST00000430051.1	TSL:5	n.153+1439T>C		intron	N/A
	LINC02923	ENST00000840899.1		n.36+2536T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108425 AN: 152060 Hom.: 39864 Cov.: 33

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.713 AC: 108474 AN: 152178 Hom.: 39882 Cov.: 33 AF XY: 0.717 AC XY: 53365 AN XY: 74402

African (AFR) AF: 0.516 AC: 21384 AN: 41460

American (AMR) AF: 0.772 AC: 11817 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3470

East Asian (EAS) AF: 0.708 AC: 3666 AN: 5180

South Asian (SAS) AF: 0.878 AC: 4229 AN: 4818

European-Finnish (FIN) AF: 0.821 AC: 8712 AN: 10608

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53514 AN: 68024

Other (OTH) AF: 0.743 AC: 1569 AN: 2112

Alfa AF: 0.764 Hom.: 42716

Bravo AF: 0.697

Asia WGS AF: 0.817 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.70
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2577756; hg19: chr2-23601556;