ENST00000421563.5:n.222+91C>T

Variant names:

• chr2-23376693-G-A
• rs2723142
• ENST00000421563.5:n.222+91C>T

Variant summary

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

The ENST00000421563.5(LINC02923):​n.222+91C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,200 control chromosomes in the GnomAD database, including 552 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 0.087 (552 hom., cov: 32)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: LINC02923 ENST00000421563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0951 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02923	NR_187213.1		n.6241+91C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02923	ENST00000421563.5	TSL:4	n.222+91C>T		intron	N/A
	LINC02923	ENST00000430051.1	TSL:5	n.296+91C>T		intron	N/A
	LINC02923	ENST00000840899.1		n.37-1233C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13151 AN: 152068 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.0894

GnomAD4 exome AF: 0.0714 AC: 1 AN: 14 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 1 AN: 10

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0865 AC: 13165 AN: 152186 Hom.: 552 Cov.: 32 AF XY: 0.0865 AC XY: 6437 AN XY: 74390

African (AFR) AF: 0.0976 AC: 4052 AN: 41528

American (AMR) AF: 0.0672 AC: 1028 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0884 AC: 307 AN: 3472

East Asian (EAS) AF: 0.0680 AC: 352 AN: 5176

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4820

European-Finnish (FIN) AF: 0.0914 AC: 966 AN: 10572

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0887 AC: 6029 AN: 68004

Other (OTH) AF: 0.0894 AC: 189 AN: 2114

Alfa AF: 0.0889 Hom.: 340

Bravo AF: 0.0880

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.29
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2723142; hg19: chr2-23599564;