Genetic Variant NM_174923.3:c.-46A>G (chr9-35658334-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_174923.3(CCDC107):c.-46A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 1,311,524 control chromosomes in the GnomAD database, including 1,312 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.063 ( 616 hom., cov: 33)

Exomes 𝑓: 0.028 ( 696 hom. )

Consequence

CCDC107
NM_174923.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.771

Publications

3 publications found

Variant links:

Genes affected

CCDC107 (HGNC:28465): (coiled-coil domain containing 107) This gene encodes a membrane protein which contains a coiled-coil domain in the central region. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2013]

CCDC107 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 9-35658334-A-G is Benign according to our data. Variant chr9-35658334-A-G is described in ClinVar as [Benign]. Clinvar id is 1234446.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC107	NM_174923.3 link	c.-46A>G		5_prime_UTR_variant	Exon 1 of 5	ENST00000426546.7	NP_777583.2	Q8WV48-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC107	ENST00000426546.7 link	c.-46A>G		5_prime_UTR_variant	Exon 1 of 5	1	NM_174923.3	ENSP00000414964.2		Q8WV48-1

Frequencies

GnomAD3 genomes

AF:

0.0630

AC:

9580

AN:

152042

Hom.:

613

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.0296

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.00637

Gnomad SAS

AF:

0.0375

Gnomad FIN

AF:

0.0127

Gnomad MID

AF:

0.0350

Gnomad NFE

AF:

0.0258

Gnomad OTH

AF:

0.0482

GnomAD2 exomes

AF:

0.0344

AC:

544

AN:

15796

AF XY:

0.0261

show subpopulations

Gnomad AFR exome

AF:

0.149

Gnomad AMR exome

AF:

0.0117

Gnomad ASJ exome

AF:

0.0122

Gnomad EAS exome

AF:

0.00534

Gnomad FIN exome

AF:

0.00989

Gnomad NFE exome

AF:

0.0242

Gnomad OTH exome

AF:

0.0391

GnomAD4 exome

AF:

0.0276

AC:

31965

AN:

1159372

Hom.:

696

Cov.:

AF XY:

0.0272

AC XY:

15166

AN XY:

556818

show subpopulations

African (AFR)

AF:

0.167

AC:

3884

AN:

23244

American (AMR)

AF:

0.0248

AC:

241

AN:

9702

Ashkenazi Jewish (ASJ)

AF:

0.0114

AC:

181

AN:

15908

East Asian (EAS)

AF:

0.00442

AC:

120

AN:

27138

South Asian (SAS)

AF:

0.0255

AC:

1046

AN:

41010

European-Finnish (FIN)

AF:

0.0153

AC:

437

AN:

28644

Middle Eastern (MID)

AF:

0.0311

AC:

107

AN:

3440

European-Non Finnish (NFE)

AF:

0.0254

AC:

24498

AN:

962938

Other (OTH)

AF:

0.0306

AC:

1451

AN:

47348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1589

3178

4768

6357

7946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0631

AC:

9601

AN:

152152

Hom.:

616

Cov.:

AF XY:

0.0602

AC XY:

4482

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.164

AC:

6817

AN:

41488

American (AMR)

AF:

0.0295

AC:

452

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

AN:

3472

East Asian (EAS)

AF:

0.00639

AC:

AN:

5164

South Asian (SAS)

AF:

0.0381

AC:

184

AN:

4824

European-Finnish (FIN)

AF:

0.0127

AC:

135

AN:

10600

Middle Eastern (MID)

AF:

0.0342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0258

AC:

1752

AN:

67978

Other (OTH)

AF:

0.0477

AC:

101

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

428

856

1284

1712

2140

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0490

Hom.:

Bravo

AF:

0.0683

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jul 07, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.6

(source)

DANN

Benign

0.41

PhyloP100

-0.77

PromoterAI

0.046

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=300/0

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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NM_174923.3:c.-46A>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over