Genetic Variant CCDC62:p.Gly10Arg (chr12-122774698-G-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_201435.5(CCDC62):c.28G>C(p.Gly10Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CCDC62
NM_201435.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.655

Publications

0 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.077459216).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201435.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC62	NM_201435.5	MANE Select	c.28G>C	p.Gly10Arg	missense	Exon 1 of 13	NP_958843.2	Q6P9F0-1
	CCDC62	NR_027918.3		n.127G>C		non_coding_transcript_exon	Exon 1 of 13

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CCDC62	ENST00000253079.11	TSL:1 MANE Select	c.28G>C	p.Gly10Arg	missense	Exon 1 of 13	ENSP00000253079.6	Q6P9F0-1
CCDC62	ENST00000392441.8	TSL:5	c.28G>C	p.Gly10Arg	missense	Exon 1 of 12	ENSP00000376236.4	Q6P9F0-2
CCDC62	ENST00000539171.1	TSL:3	c.28G>C	p.Gly10Arg	missense	Exon 1 of 3	ENSP00000439893.1	F5H0F1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1104694

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

523390

African (AFR)

AF:

0.00

AC:

AN:

23450

American (AMR)

AF:

0.00

AC:

AN:

8890

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14798

East Asian (EAS)

AF:

0.00

AC:

AN:

27256

South Asian (SAS)

AF:

0.00

AC:

AN:

21792

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36018

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4558

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

923762

Other (OTH)

AF:

0.00

AC:

AN:

44170

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.64

DEOGEN2

Benign

0.015

Eigen

Benign

-0.89

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.18

LIST_S2

Benign

0.65

M_CAP

Benign

0.027

MetaRNN

Benign

0.077

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.20

PhyloP100

0.66

PrimateAI

Uncertain

0.61

PROVEAN

Benign

0.080

REVEL

Benign

0.029

Sift

Benign

0.69

Sift4G

Benign

0.71

Polyphen

0.0030

Vest4

0.052

MutPred

0.25

Gain of loop (P = 0.0013)

MVP

0.26

MPC

0.29

ClinPred

0.13

GERP RS

0.65

PromoterAI

0.022

Neutral

(source)

Varity_R

0.035

gMVP

0.41

Mutation Taster

=96/4

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over