rs2723142

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.308
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
LINC02923NR_187213.1 linkuse as main transcriptn.6241+91C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02923ENST00000421563.5 linkuse as main transcriptn.222+91C>T intron_variant 4
LINC02923ENST00000430051.1 linkuse as main transcriptn.296+91C>T intron_variant 5

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2723142; hg19: chr2-23599564; API