dbSNP rs6005881: CCDC117:c.*819A>G (chr22-28787145-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_173510.4(CCDC117):c.*819A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,292 control chromosomes in the GnomAD database, including 16,087 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 0.43 ( 16066 hom., cov: 31)

Exomes 𝑓: 0.37 ( 21 hom. )

Consequence

CCDC117
NM_173510.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185

Publications

16 publications found

Variant links:

Genes affected

CCDC117 (HGNC:26599): (coiled-coil domain containing 117)

CCDC117 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173510.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC117	NM_173510.4	MANE Select	c.*819A>G	3_prime_UTR	Exon 5 of 5	NP_775781.1
CCDC117	NM_001284263.2		c.*819A>G	3_prime_UTR	Exon 4 of 4	NP_001271192.1
CCDC117	NM_001284264.2		c.*819A>G	3_prime_UTR	Exon 4 of 4	NP_001271193.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC117	ENST00000249064.9	TSL:1 MANE Select	c.*819A>G	3_prime_UTR	Exon 5 of 5	ENSP00000249064.4
CCDC117	ENST00000448492.6	TSL:2	c.*819A>G	3_prime_UTR	Exon 4 of 4	ENSP00000389478.2
CCDC117	ENST00000421503.6	TSL:2	c.*819A>G	3_prime_UTR	Exon 4 of 4	ENSP00000387827.2

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65154

AN:

151758

Hom.:

16015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.657

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.312

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.676

Gnomad SAS

AF:

0.538

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.393

GnomAD4 exome

AF:

0.370

AC:

154

AN:

416

Hom.:

Cov.:

AF XY:

0.357

AC XY:

AN XY:

252

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:

0.371

AC:

153

AN:

412

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.430

AC:

65270

AN:

151876

Hom.:

16066

Cov.:

AF XY:

0.432

AC XY:

32028

AN XY:

74216

show subpopulations

African (AFR)

AF:

0.658

AC:

27227

AN:

41404

American (AMR)

AF:

0.313

AC:

4774

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.332

AC:

1148

AN:

3456

East Asian (EAS)

AF:

0.676

AC:

3486

AN:

5158

South Asian (SAS)

AF:

0.537

AC:

2586

AN:

4816

European-Finnish (FIN)

AF:

0.373

AC:

3922

AN:

10528

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.309

AC:

21013

AN:

67946

Other (OTH)

AF:

0.398

AC:

841

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1700

3400

5100

6800

8500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

592

1184

1776

2368

2960

<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:

0.343

Hom.:

12328

Bravo

AF:

0.432

Asia WGS

AF:

0.619

AC:

2152

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

(source)

DANN

Benign

0.39

PhyloP100

-0.18

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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over