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GeneBe

rs4408325

Positions:

Variant summary

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

The ENST00000655771.2(CCDC15-DT):​n.564-129A>T 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 0.709 in 152,000 control chromosomes in the GnomAD database, including 39,207 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 0.71 ( 39207 hom., cov: 30)

Consequence

CCDC15-DT
ENST00000655771.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.115
Variant links:
Genes affected
CCDC15-DT (HGNC:54193): (CCDC15 divergent transcript)

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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=-0.9).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCDC15-DTXR_948134.3 linkuse as main transcriptn.511-129A>T intron_variant, non_coding_transcript_variant
CCDC15-DTXR_948132.3 linkuse as main transcriptn.511-129A>T intron_variant, non_coding_transcript_variant
CCDC15-DTXR_948133.3 linkuse as main transcriptn.511-129A>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCDC15-DTENST00000655771.2 linkuse as main transcriptn.564-129A>T intron_variant, non_coding_transcript_variant
CCDC15-DTENST00000649496.1 linkuse as main transcriptn.75-129A>T intron_variant, non_coding_transcript_variant
CCDC15-DTENST00000667169.1 linkuse as main transcriptn.48-129A>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.709
AC:
107713
AN:
151882
Hom.:
39156
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.839
Gnomad AMI
AF:
0.648
Gnomad AMR
AF:
0.657
Gnomad ASJ
AF:
0.829
Gnomad EAS
AF:
0.930
Gnomad SAS
AF:
0.848
Gnomad FIN
AF:
0.637
Gnomad MID
AF:
0.797
Gnomad NFE
AF:
0.620
Gnomad OTH
AF:
0.717
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:
0.709
AC:
107825
AN:
152000
Hom.:
39207
Cov.:
30
AF XY:
0.713
AC XY:
52997
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.840
Gnomad4 AMR
AF:
0.656
Gnomad4 ASJ
AF:
0.829
Gnomad4 EAS
AF:
0.930
Gnomad4 SAS
AF:
0.848
Gnomad4 FIN
AF:
0.637
Gnomad4 NFE
AF:
0.620
Gnomad4 OTH
AF:
0.720
Alfa
AF:
0.512
Hom.:
1247
Bravo
AF:
0.715
Asia WGS
AF:
0.895
AC:
3112
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.9
DANN
Benign
0.50

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: rs4408325; hg19: chr11-124821575; API