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GeneBe

rs2845384

chr22-17051559-G-A

Variant summary

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

The NR_015352.2(CECR7):n.1006+4133G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,196 control chromosomes in the GnomAD database, including 53,562 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 0.83 ( 53562 hom., cov: 32)

Consequence

CECR7
NR_015352.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.751
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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CECR7NR_015352.2 linkuse as main transcriptn.1006+4133G>A intron_variant, non_coding_transcript_variant
CECR7NR_152825.1 linkuse as main transcriptn.1006+4133G>A intron_variant, non_coding_transcript_variant
CECR7NR_152826.1 linkuse as main transcriptn.1006+4133G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000441006.5 linkuse as main transcriptn.1006+4133G>A intron_variant, non_coding_transcript_variant 1
ENST00000609932.5 linkuse as main transcriptn.337+4133G>A intron_variant, non_coding_transcript_variant 2
ENST00000414401.5 linkuse as main transcriptn.364+4133G>A intron_variant, non_coding_transcript_variant 4
ENST00000609596.1 linkuse as main transcriptn.294+4129G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.832
AC:
126570
AN:
152078
Hom.:
53512
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.960
Gnomad AMI
AF:
0.867
Gnomad AMR
AF:
0.660
Gnomad ASJ
AF:
0.812
Gnomad EAS
AF:
0.580
Gnomad SAS
AF:
0.761
Gnomad FIN
AF:
0.843
Gnomad MID
AF:
0.930
Gnomad NFE
AF:
0.816
Gnomad OTH
AF:
0.815
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.832
AC:
126673
AN:
152196
Hom.:
53562
Cov.:
32
AF XY:
0.829
AC XY:
61672
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.960
Gnomad4 AMR
AF:
0.659
Gnomad4 ASJ
AF:
0.812
Gnomad4 EAS
AF:
0.580
Gnomad4 SAS
AF:
0.762
Gnomad4 FIN
AF:
0.843
Gnomad4 NFE
AF:
0.816
Gnomad4 OTH
AF:
0.813
Alfa
AF:
0.837
Hom.:
7833
Bravo
AF:
0.821
Asia WGS
AF:
0.664
AC:
2309
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
1.9
Dann
Benign
0.71
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs2845384; hg19: chr22-17532449; API