Variant 12-411810-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_032358.4(CCDC77):c.102A>G(p.Ala34Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00684 in 1,614,088 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0071 ( 42 hom. )

Consequence

CCDC77
NM_032358.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.283

Variant links:

Genes affected

CCDC77 (HGNC:28203): (coiled-coil domain containing 77) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

CCDC77 links:

CCDC77 (HGNC:):

CCDC77 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 12-411810-A-G is Benign according to our data. Variant chr12-411810-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2642563.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.283 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC77	NM_032358.4 linkuse as main transcript	c.102A>G	p.Ala34Ala	synonymous_variant	4/13	ENST00000239830.9	NP_115734.1	Q9BR77-1
CCDC77	NM_001130146.2 linkuse as main transcript	c.6A>G	p.Ala2Ala	synonymous_variant	3/12		NP_001123618.1	Q9BR77-2
CCDC77	NM_001130147.2 linkuse as main transcript	c.6A>G	p.Ala2Ala	synonymous_variant	3/12		NP_001123619.1	Q9BR77-2
CCDC77	NM_001130148.2 linkuse as main transcript	c.6A>G	p.Ala2Ala	synonymous_variant	2/11		NP_001123620.1	Q9BR77-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC77	ENST00000239830.9 linkuse as main transcript	c.102A>G	p.Ala34Ala	synonymous_variant	4/13	2	NM_032358.4	ENSP00000239830.4		Q9BR77-1

Frequencies

GnomAD3 genomes

AF:

0.00474

AC:

721

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00426

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00810

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00451

AC:

1135

AN:

251480

Hom.:

AF XY:

0.00477

AC XY:

648

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00393

Gnomad ASJ exome

AF:

0.00198

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00166

Gnomad NFE exome

AF:

0.00775

Gnomad OTH exome

AF:

0.00668

GnomAD4 exome

AF:

0.00705

AC:

10313

AN:

1461868

Hom.:

Cov.:

AF XY:

0.00678

AC XY:

4932

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00155

Gnomad4 AMR exome

AF:

0.00402

Gnomad4 ASJ exome

AF:

0.00165

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000580

Gnomad4 FIN exome

AF:

0.00197

Gnomad4 NFE exome

AF:

0.00857

Gnomad4 OTH exome

AF:

0.00641

GnomAD4 genome

AF:

0.00474

AC:

721

AN:

152220

Hom.:

Cov.:

AF XY:

0.00414

AC XY:

308

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.00144

Gnomad4 AMR

AF:

0.00426

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00810

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00668

Hom.:

Bravo

AF:

0.00504

EpiCase

AF:

0.00812

EpiControl

AF:

0.0103

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

Mar 01, 2023

CCDC77: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.82

DANN

Benign

0.34

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.

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