rs2577704

Variant names:

• chr2-23369274-G-A
• rs2577704
• NR_187213.1:n.7149+5366C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-23369274-G-A
• chr2-23369274-G-C
• chr2-23369274-G-T

Variant summary

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

The NR_187213.1(LINC02923):​n.7149+5366C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 151,506 control chromosomes in the GnomAD database, including 771 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 0.099 (771 hom., cov: 31)
• Consequence: LINC02923 NR_187213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187213.1. 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.7149+5366C>T		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0990 AC: 14994 AN: 151388 Hom.: 767 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0711

Gnomad ASJ AF: 0.0846

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0991 AC: 15017 AN: 151506 Hom.: 771 Cov.: 31 AF XY: 0.0991 AC XY: 7333 AN XY: 74020

African (AFR) AF: 0.145 AC: 5966 AN: 41230

American (AMR) AF: 0.0711 AC: 1080 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.0846 AC: 293 AN: 3464

East Asian (EAS) AF: 0.0690 AC: 354 AN: 5128

South Asian (SAS) AF: 0.0432 AC: 206 AN: 4772

European-Finnish (FIN) AF: 0.0914 AC: 958 AN: 10486

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0871 AC: 5916 AN: 67928

Other (OTH) AF: 0.0993 AC: 209 AN: 2104

Alfa AF: 0.0926 Hom.: 2735

Bravo AF: 0.102

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.097
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2577704; hg19: chr2-23592145;