rs16872762

Variant summary

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

The NM_001134848.2(CCDC152):​c.*42A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,543,092 control chromosomes in the GnomAD database, including 1,734 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 0.018 ( 143 hom., cov: 33)
Exomes 𝑓: 0.022 ( 1591 hom. )

Consequence

CCDC152
NM_001134848.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.457
Variant links:
Genes affected
CCDC152 (HGNC:34438): (coiled-coil domain containing 152)

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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC152NM_001134848.2 linkuse as main transcriptc.*42A>G 3_prime_UTR_variant 9/9 ENST00000361970.10 NP_001128320.1
CCDC152XM_047416584.1 linkuse as main transcriptc.*42A>G 3_prime_UTR_variant 9/9 XP_047272540.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC152ENST00000361970.10 linkuse as main transcriptc.*42A>G 3_prime_UTR_variant 9/91 NM_001134848.2 ENSP00000354888 P1Q4G0S7-1
CCDC152ENST00000388827.4 linkuse as main transcriptc.*42A>G 3_prime_UTR_variant 7/72 ENSP00000373479 Q4G0S7-2

Frequencies

GnomAD3 genomes
AF:
0.0179
AC:
2726
AN:
152220
Hom.:
143
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00429
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0166
Gnomad ASJ
AF:
0.00893
Gnomad EAS
AF:
0.138
Gnomad SAS
AF:
0.175
Gnomad FIN
AF:
0.00367
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.00904
Gnomad OTH
AF:
0.0182
GnomAD3 exomes
AF:
0.0432
AC:
6434
AN:
149048
Hom.:
479
AF XY:
0.0513
AC XY:
4045
AN XY:
78840
show subpopulations
Gnomad AFR exome
AF:
0.00399
Gnomad AMR exome
AF:
0.0252
Gnomad ASJ exome
AF:
0.0105
Gnomad EAS exome
AF:
0.136
Gnomad SAS exome
AF:
0.173
Gnomad FIN exome
AF:
0.00310
Gnomad NFE exome
AF:
0.0101
Gnomad OTH exome
AF:
0.0270
GnomAD4 exome
AF:
0.0220
AC:
30655
AN:
1390754
Hom.:
1591
Cov.:
30
AF XY:
0.0262
AC XY:
17998
AN XY:
685648
show subpopulations
Gnomad4 AFR exome
AF:
0.00338
Gnomad4 AMR exome
AF:
0.0247
Gnomad4 ASJ exome
AF:
0.0102
Gnomad4 EAS exome
AF:
0.0959
Gnomad4 SAS exome
AF:
0.169
Gnomad4 FIN exome
AF:
0.00289
Gnomad4 NFE exome
AF:
0.0101
Gnomad4 OTH exome
AF:
0.0312
GnomAD4 genome
AF:
0.0179
AC:
2729
AN:
152338
Hom.:
143
Cov.:
33
AF XY:
0.0206
AC XY:
1533
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.00430
Gnomad4 AMR
AF:
0.0171
Gnomad4 ASJ
AF:
0.00893
Gnomad4 EAS
AF:
0.136
Gnomad4 SAS
AF:
0.176
Gnomad4 FIN
AF:
0.00367
Gnomad4 NFE
AF:
0.00904
Gnomad4 OTH
AF:
0.0180
Alfa
AF:
0.0133
Hom.:
13
Bravo
AF:
0.0158
Asia WGS
AF:
0.145
AC:
503
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.3
DANN
Benign
0.45

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: rs16872762; hg19: chr5-42799925; API