Genetic Variant CCDC158:c.2882+122G>T (chr4-76332310-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001394954.1(CCDC158):c.2882+122G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000018 in 556,238 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000018 ( 0 hom. )

Consequence

CCDC158
NM_001394954.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.101

Publications

0 publications found

Variant links:

Genes affected

CCDC158 (HGNC:26374): (coiled-coil domain containing 158)

CCDC158 Gene-Disease associations (from GenCC):

renal tubule disorder
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

CCDC158 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC158	NM_001394954.1 link	c.2882+122G>T		intron_variant	Intron 20 of 24	ENST00000682701.1	NP_001381883.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CCDC158	ENST00000682701.1 link	c.2882+122G>T	intron_variant	Intron 20 of 24		NM_001394954.1	ENSP00000507278.1
CCDC158	ENST00000504667.2 link	n.2748+122G>T	intron_variant	Intron 8 of 12	1
CCDC158	ENST00000388914.7 link	c.2870+122G>T	intron_variant	Intron 19 of 23	5		ENSP00000373566.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000180

AC:

AN:

556238

Hom.:

AF XY:

0.00

AC XY:

AN XY:

299804

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11854

American (AMR)

AF:

0.00

AC:

AN:

17016

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17202

East Asian (EAS)

AF:

0.0000357

AC:

AN:

28020

South Asian (SAS)

AF:

0.00

AC:

AN:

51168

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45668

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3548

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

353046

Other (OTH)

AF:

0.00

AC:

AN:

28716

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.3

(source)

DANN

Benign

0.79

PhyloP100

0.10

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over