chr22-34943863-T-G

Variant summary

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

The NR_138042.1(LINC02885):​n.199-41100A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,980 control chromosomes in the GnomAD database, including 20,308 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 0.50 ( 20308 hom., cov: 32)

Consequence

LINC02885
NR_138042.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0320
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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02885NR_138042.1 linkuse as main transcriptn.199-41100A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02885ENST00000668433.1 linkuse as main transcriptn.203-41100A>C intron_variant
LINC02885ENST00000700833.1 linkuse as main transcriptn.38-41100A>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.500
AC:
75931
AN:
151862
Hom.:
20291
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.299
Gnomad AMI
AF:
0.580
Gnomad AMR
AF:
0.529
Gnomad ASJ
AF:
0.577
Gnomad EAS
AF:
0.603
Gnomad SAS
AF:
0.704
Gnomad FIN
AF:
0.608
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.571
Gnomad OTH
AF:
0.518
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.500
AC:
75995
AN:
151980
Hom.:
20308
Cov.:
32
AF XY:
0.509
AC XY:
37798
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.300
Gnomad4 AMR
AF:
0.529
Gnomad4 ASJ
AF:
0.577
Gnomad4 EAS
AF:
0.603
Gnomad4 SAS
AF:
0.705
Gnomad4 FIN
AF:
0.608
Gnomad4 NFE
AF:
0.571
Gnomad4 OTH
AF:
0.522
Alfa
AF:
0.546
Hom.:
4671
Bravo
AF:
0.482
Asia WGS
AF:
0.667
AC:
2318
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
6.4
DANN
Benign
0.39

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: rs10483186; hg19: chr22-35339852; API