22-41822852-A-G

Variant summary

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

The NM_024821.5(CCDC134):​c.565-2846A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,072 control chromosomes in the GnomAD database, including 12,755 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 0.38 ( 12755 hom., cov: 32)

Consequence

CCDC134
NM_024821.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.242
Variant links:
Genes affected
CCDC134 (HGNC:26185): (coiled-coil domain containing 134) Predicted to act upstream of or within angiogenesis and animal organ development. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC134NM_024821.5 linkc.565-2846A>G intron_variant Intron 6 of 6 ENST00000255784.6 NP_079097.1 Q9H6E4
CCDC134NM_001382346.1 linkc.565-2846A>G intron_variant Intron 7 of 7 NP_001369275.1
CCDC134NM_001304797.2 linkc.226-2846A>G intron_variant Intron 3 of 3 NP_001291726.1 B0QY51B4DRL0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC134ENST00000255784.6 linkc.565-2846A>G intron_variant Intron 6 of 6 1 NM_024821.5 ENSP00000255784.5 Q9H6E4
CCDC134ENST00000402061.7 linkc.226-2846A>G intron_variant Intron 3 of 3 2 ENSP00000385803.3 B0QY51

Frequencies

GnomAD3 genomes
AF:
0.379
AC:
57653
AN:
151954
Hom.:
12697
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.576
Gnomad AMI
AF:
0.325
Gnomad AMR
AF:
0.515
Gnomad ASJ
AF:
0.422
Gnomad EAS
AF:
0.249
Gnomad SAS
AF:
0.363
Gnomad FIN
AF:
0.226
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.263
Gnomad OTH
AF:
0.356
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.380
AC:
57776
AN:
152072
Hom.:
12755
Cov.:
32
AF XY:
0.380
AC XY:
28275
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.578
Gnomad4 AMR
AF:
0.516
Gnomad4 ASJ
AF:
0.422
Gnomad4 EAS
AF:
0.248
Gnomad4 SAS
AF:
0.363
Gnomad4 FIN
AF:
0.226
Gnomad4 NFE
AF:
0.264
Gnomad4 OTH
AF:
0.352
Alfa
AF:
0.289
Hom.:
11127
Bravo
AF:
0.414
Asia WGS
AF:
0.331
AC:
1149
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.0
DANN
Benign
0.89

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: rs7364180; hg19: chr22-42218856; API