Menu
GeneBe

rs1869485

Variant summary

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

The NM_024611.6(ICE2):c.943+597C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,892 control chromosomes in the GnomAD database, including 22,572 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 0.52 ( 22572 hom., cov: 32)

Consequence

ICE2
NM_024611.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.740
Variant links:
Genes affected
ICE2 (HGNC:29885): (interactor of little elongation complex ELL subunit 2) This gene encodes a protein component of the little elongation complex (LEC), which plays a role in small nuclear RNA (snRNA) transcription. The LEC regulates snRNA transcription by enhancing both RNA Polymerase II occupancy and transcriptional elongation. The encoded protein and other LEC components have been shown to localize to Cajal bodies, which are sites of ribonucleoprotein (RNP) complex assembly. Pseudogenes of this gene have been identified on chromosomes 3 and 4. [provided by RefSeq, May 2017]

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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ICE2NM_024611.6 linkuse as main transcriptc.943+597C>T intron_variant ENST00000261520.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ICE2ENST00000261520.9 linkuse as main transcriptc.943+597C>T intron_variant 1 NM_024611.6 P1Q659A1-1
ICE2ENST00000558512.5 linkuse as main transcriptc.943+597C>T intron_variant 1
ICE2ENST00000561114.5 linkuse as main transcriptc.943+597C>T intron_variant 1
ICE2ENST00000558181.5 linkuse as main transcriptc.*561+597C>T intron_variant, NMD_transcript_variant 1 Q659A1-2

Frequencies

GnomAD3 genomes
AF:
0.521
AC:
79104
AN:
151774
Hom.:
22550
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.291
Gnomad AMI
AF:
0.707
Gnomad AMR
AF:
0.597
Gnomad ASJ
AF:
0.497
Gnomad EAS
AF:
0.836
Gnomad SAS
AF:
0.781
Gnomad FIN
AF:
0.714
Gnomad MID
AF:
0.310
Gnomad NFE
AF:
0.572
Gnomad OTH
AF:
0.503
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.521
AC:
79150
AN:
151892
Hom.:
22572
Cov.:
32
AF XY:
0.534
AC XY:
39653
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.291
Gnomad4 AMR
AF:
0.597
Gnomad4 ASJ
AF:
0.497
Gnomad4 EAS
AF:
0.836
Gnomad4 SAS
AF:
0.781
Gnomad4 FIN
AF:
0.714
Gnomad4 NFE
AF:
0.572
Gnomad4 OTH
AF:
0.508
Alfa
AF:
0.569
Hom.:
11570
Bravo
AF:
0.498
Asia WGS
AF:
0.780
AC:
2709
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
Cadd
Benign
5.1
Dann
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs1869485; hg19: chr15-60746605; API