Genetic Variant CC2D1B:c.*709C>T (chr1-52352516-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001330585.2(CC2D1B):c.*709C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,462 control chromosomes in the GnomAD database, including 27,913 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 27858 hom., cov: 32)

Exomes 𝑓: 0.47 ( 55 hom. )

Consequence

CC2D1B
NM_001330585.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.995

Publications

31 publications found

Variant links:

Genes affected

CC2D1B (HGNC:29386): (coiled-coil and C2 domain containing 1B) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CC2D1B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330585.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CC2D1B	NM_001330585.2	MANE Select	c.*709C>T		3_prime_UTR	Exon 25 of 25	NP_001317514.1
	CC2D1B	NM_032449.3		c.*1003C>T		3_prime_UTR	Exon 24 of 24	NP_115825.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CC2D1B	ENST00000284376.8	TSL:5 MANE Select	c.*709C>T	3_prime_UTR	Exon 25 of 25	ENSP00000284376.3
CC2D1B	ENST00000371586.6	TSL:5	c.*1003C>T	3_prime_UTR	Exon 24 of 24	ENSP00000360642.2
CC2D1B	ENST00000470844.5	TSL:5	n.247+1002C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87193

AN:

151910

Hom.:

27810

Cov.:

show subpopulations

Gnomad AFR

AF:

0.853

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.531

GnomAD4 exome

AF:

0.465

AC:

202

AN:

434

Hom.:

Cov.:

AF XY:

0.504

AC XY:

132

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.458

AC:

195

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.574

AC:

87292

AN:

152028

Hom.:

27858

Cov.:

AF XY:

0.564

AC XY:

41924

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.853

AC:

35408

AN:

41512

American (AMR)

AF:

0.408

AC:

6229

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.544

AC:

1888

AN:

3472

East Asian (EAS)

AF:

0.160

AC:

831

AN:

5178

South Asian (SAS)

AF:

0.523

AC:

2510

AN:

4802

European-Finnish (FIN)

AF:

0.435

AC:

4588

AN:

10536

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.503

AC:

34178

AN:

67948

Other (OTH)

AF:

0.528

AC:

1109

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1657

3314

4972

6629

8286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.524

Hom.:

38748

Bravo

AF:

0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

5.1

(source)

DANN

Benign

0.28

PhyloP100

-0.99

Mutation Taster

=100/0

polymorphism (auto)

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over