Variant 12-122777496-C-T 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_201435.5(CCDC62):c.42C>T(p.Ile14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,606,116 control chromosomes in the GnomAD database, including 153 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0084 ( 5 hom., cov: 32)

Exomes 𝑓: 0.012 ( 148 hom. )

Consequence

CCDC62
NM_201435.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.391

Variant links:

Genes affected

CCDC62 (HGNC:30723): (coiled-coil domain containing 62) Enables estrogen receptor binding activity and nuclear receptor coactivator activity. Involved in cellular response to estradiol stimulus and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CCDC62 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 12-122777496-C-T is Benign according to our data. Variant chr12-122777496-C-T is described in ClinVar as [Benign]. Clinvar id is 2643506.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.391 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC62	NM_201435.5 linkuse as main transcript	c.42C>T	p.Ile14=	synonymous_variant	2/13	ENST00000253079.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC62	ENST00000253079.11 linkuse as main transcript	c.42C>T	p.Ile14=	synonymous_variant	2/13	1	NM_201435.5	P3	Q6P9F0-1

Frequencies

GnomAD3 genomes

AF:

0.00843

AC:

1282

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00232

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00767

Gnomad ASJ

AF:

0.00865

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00594

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.00955

GnomAD3 exomes

AF:

0.00803

AC:

1988

AN:

247460

Hom.:

AF XY:

0.00818

AC XY:

1093

AN XY:

133654

show subpopulations

Gnomad AFR exome

AF:

0.00216

Gnomad AMR exome

AF:

0.00414

Gnomad ASJ exome

AF:

0.00827

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00183

Gnomad FIN exome

AF:

0.00552

Gnomad NFE exome

AF:

0.0133

Gnomad OTH exome

AF:

0.00978

GnomAD4 exome

AF:

0.0123

AC:

17914

AN:

1453866

Hom.:

148

Cov.:

AF XY:

0.0119

AC XY:

8592

AN XY:

722166

show subpopulations

Gnomad4 AFR exome

AF:

0.00187

Gnomad4 AMR exome

AF:

0.00481

Gnomad4 ASJ exome

AF:

0.00782

Gnomad4 EAS exome

AF:

0.0000506

Gnomad4 SAS exome

AF:

0.00209

Gnomad4 FIN exome

AF:

0.00593

Gnomad4 NFE exome

AF:

0.0147

Gnomad4 OTH exome

AF:

0.0102

GnomAD4 genome

AF:

0.00843

AC:

1283

AN:

152250

Hom.:

Cov.:

AF XY:

0.00763

AC XY:

568

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00231

Gnomad4 AMR

AF:

0.00766

Gnomad4 ASJ

AF:

0.00865

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00594

Gnomad4 NFE

AF:

0.0139

Gnomad4 OTH

AF:

0.00945

Alfa

AF:

0.0112

Hom.:

Bravo

AF:

0.00901

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0139

EpiControl

AF:

0.0138

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

CCDC62: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

6.7

DANN

Benign

0.84

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