rs2723142

Positions:

• chr2-23376693-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02923	NR_187213.1	n.6241+91C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02923	ENST00000421563.5	n.222+91C>T		intron_variant		4
LINC02923	ENST00000430051.1	n.296+91C>T		intron_variant		5

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.100

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

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.0884

Gnomad4 EAS AF: 0.0680

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0887 Hom.: 312

Bravo AF: 0.0880

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2723142; hg19: chr2-23599564;