Variant chr7-128791523-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001367764.1(CCDC136):c.30A>C(p.Gly10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00526 in 1,290,490 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0054 ( 22 hom. )

Consequence

CCDC136
NM_001367764.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.11

Variant links:

Genes affected

CCDC136 (HGNC:22225): (coiled-coil domain containing 136) Predicted to be involved in acrosome assembly and single fertilization. Predicted to be integral component of membrane. Predicted to be active in acrosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]

CCDC136 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BP6

Variant 7-128791523-A-C is Benign according to our data. Variant chr7-128791523-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2657988.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.12 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
CCDC136	NM_001367764.1 linkuse as main transcript	c.30A>C	p.Gly10=	synonymous_variant	1/18	NP_001354693.1
CCDC136	NM_001363423.2 linkuse as main transcript	c.30A>C	p.Gly10=	synonymous_variant	1/16	NP_001350352.1
CCDC136	NM_001363424.2 linkuse as main transcript	c.30A>C	p.Gly10=	synonymous_variant	1/16	NP_001350353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	Appris	UniProt
CCDC136	ENST00000464832.5 linkuse as main transcript	c.30A>C	p.Gly10=	synonymous_variant	1/10	5	ENSP00000419515	P2
CCDC136	ENST00000378685.8 linkuse as main transcript	c.30A>C	p.Gly10=	synonymous_variant	1/10	2	ENSP00000367956	A2	Q96JN2-3
CCDC136	ENST00000459946.5 linkuse as main transcript	c.-205A>C		5_prime_UTR_variant	1/5	3	ENSP00000417708

Frequencies

GnomAD3 genomes

AF:

0.00402

AC:

610

AN:

151652

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00577

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00623

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00627

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00502

AC:

AN:

6174

Hom.:

AF XY:

0.00339

AC XY:

AN XY:

3248

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00620

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00543

AC:

6181

AN:

1138728

Hom.:

Cov.:

AF XY:

0.00531

AC XY:

2916

AN XY:

549288

show subpopulations

Gnomad4 AFR exome

AF:

0.000685

Gnomad4 AMR exome

AF:

0.00368

Gnomad4 ASJ exome

AF:

0.00350

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00384

Gnomad4 FIN exome

AF:

0.00162

Gnomad4 NFE exome

AF:

0.00598

Gnomad4 OTH exome

AF:

0.00396

GnomAD4 genome

AF:

0.00402

AC:

610

AN:

151762

Hom.:

Cov.:

AF XY:

0.00411

AC XY:

305

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.00121

Gnomad4 AMR

AF:

0.00367

Gnomad4 ASJ

AF:

0.00577

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00623

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.00627

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00464

Hom.:

Bravo

AF:

0.00395

Asia WGS

AF:

0.00145

AC:

AN:

3464

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

CCDC136: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over