Variant 19-46016077-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001267723.2(CCDC61):c.869C>T(p.Pro290Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 1,234,706 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0033 ( 7 hom. )

Consequence

CCDC61
NM_001267723.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.781

Variant links:

Genes affected

CCDC61 (HGNC:33629): (coiled-coil domain containing 61) Enables identical protein binding activity and microtubule binding activity. Involved in centriole assembly and mitotic spindle assembly. Located in centriolar satellite and ciliary basal body. Part of centriolar subdistal appendage. [provided by Alliance of Genome Resources, Apr 2022]

CCDC61 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0056904852).

BP6

Variant 19-46016077-C-T is Benign according to our data. Variant chr19-46016077-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 781453.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC61	NM_001267723.2 linkuse as main transcript	c.869C>T	p.Pro290Leu	missense_variant	8/14	ENST00000595358.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC61	ENST00000595358.5 linkuse as main transcript	c.869C>T	p.Pro290Leu	missense_variant	8/14	5	NM_001267723.2	P1	Q9Y6R9-1
CCDC61	ENST00000536603.5 linkuse as main transcript	c.552-617C>T		intron_variant		1			Q9Y6R9-2
CCDC61	ENST00000594087.1 linkuse as main transcript	c.552-617C>T		intron_variant		5			Q9Y6R9-2

Frequencies

GnomAD3 genomes

AF:

0.00184

AC:

279

AN:

152018

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000652

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000566

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00352

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00622

AC:

AN:

482

Hom.:

AF XY:

0.00654

AC XY:

AN XY:

306

show subpopulations

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00915

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00333

AC:

3602

AN:

1082582

Hom.:

Cov.:

AF XY:

0.00322

AC XY:

1648

AN XY:

511226

show subpopulations

Gnomad4 AFR exome

AF:

0.000567

Gnomad4 AMR exome

AF:

0.000357

Gnomad4 ASJ exome

AF:

0.0000696

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000504

Gnomad4 FIN exome

AF:

0.00145

Gnomad4 NFE exome

AF:

0.00376

Gnomad4 OTH exome

AF:

0.00192

GnomAD4 genome

AF:

0.00183

AC:

279

AN:

152124

Hom.:

Cov.:

AF XY:

0.00159

AC XY:

118

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.000650

Gnomad4 AMR

AF:

0.000262

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000566

Gnomad4 NFE

AF:

0.00352

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.000866

Hom.:

Bravo

AF:

0.00182

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00104

AC:

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

Invitae

Nov 27, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.69

CADD

Benign

7.3

DANN

Benign

0.95

DEOGEN2

Benign

0.00076

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.58

M_CAP

Benign

0.022

MetaRNN

Benign

0.0057

MutationAssessor

Benign

0.55

MutationTaster

Benign

1.0

N;N

PrimateAI

Uncertain

0.71

Sift4G

Benign

0.29

Vest4

0.18

MVP

0.67

MPC

0.27

GERP RS

-0.21

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.030

gMVP

0.35

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