dbSNP rs9797: CCDC25:n.*2330C>T (chr8-27734332-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 ENST00000520486.5(CCDC25):n.*2330C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,036 control chromosomes in the GnomAD database, including 14,324 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 0.42 ( 14321 hom., cov: 32)

Exomes 𝑓: 0.50 ( 3 hom. )

Consequence

CCDC25
ENST00000520486.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.642

Publications

25 publications found

Variant links:

Genes affected

CCDC25 (HGNC:25591): (coiled-coil domain containing 25) Enables DNA binding activity. Involved in positive regulation of cell motility. Located in endomembrane system. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CCDC25 links:

ENSG00000253875 (HGNC:):

ENSG00000253875 links:

SCARA3 (HGNC:19000): (scavenger receptor class A member 3) This gene encodes a macrophage scavenger receptor-like protein. This protein has been shown to deplete reactive oxygen species, and thus play an important role in protecting cells from oxidative stress. The expression of this gene is induced by oxidative stress. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

SCARA3 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=-0.74).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520486.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC25	NM_018246.3	MANE Select	c.*1884C>T	3_prime_UTR	Exon 9 of 9	NP_060716.2
CCDC25	NR_130761.2		n.2461C>T	non_coding_transcript_exon	Exon 7 of 7
CCDC25	NR_130762.2		n.2455C>T	non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC25	ENST00000520486.5	TSL:1	n.*2330C>T	non_coding_transcript_exon	Exon 8 of 8	ENSP00000427714.1
CCDC25	ENST00000356537.9	TSL:1 MANE Select	c.*1884C>T	3_prime_UTR	Exon 9 of 9	ENSP00000348933.4
CCDC25	ENST00000520486.5	TSL:1	n.*2330C>T	3_prime_UTR	Exon 8 of 8	ENSP00000427714.1

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

64451

AN:

151898

Hom.:

14325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.352

Gnomad AMI

AF:

0.464

Gnomad AMR

AF:

0.383

Gnomad ASJ

AF:

0.558

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.433

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

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:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.424

AC:

64471

AN:

152018

Hom.:

14321

Cov.:

AF XY:

0.426

AC XY:

31678

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.352

AC:

14580

AN:

41440

American (AMR)

AF:

0.382

AC:

5834

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.558

AC:

1937

AN:

3472

East Asian (EAS)

AF:

0.121

AC:

626

AN:

5186

South Asian (SAS)

AF:

0.418

AC:

2015

AN:

4820

European-Finnish (FIN)

AF:

0.534

AC:

5629

AN:

10540

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.476

AC:

32371

AN:

67976

Other (OTH)

AF:

0.429

AC:

907

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1860

3720

5581

7441

9301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

604

1208

1812

2416

3020

<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:

0.459

Hom.:

46118

Bravo

AF:

0.407

Asia WGS

AF:

0.258

AC:

901

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

8.5

(source)

DANN

Benign

0.80

PhyloP100

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over