Variant chr9-35658334-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCDC107	NM_174923.3 linkuse as main transcript	c.-46A>G		5_prime_UTR_variant	1/5	ENST00000426546.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC107	ENST00000426546.7 linkuse as main transcript	c.-46A>G		5_prime_UTR_variant	1/5	1	NM_174923.3	A2	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

GnomAD3 exomes

AF:

0.0344

AC:

544

AN:

15796

Hom.:

AF XY:

0.0261

AC XY:

197

AN XY:

7546

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 SAS exome

AF:

0.0244

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

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

0.0248

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.00442

Gnomad4 SAS exome

AF:

0.0255

Gnomad4 FIN exome

AF:

0.0153

Gnomad4 NFE exome

AF:

0.0254

Gnomad4 OTH exome

AF:

0.0306

GnomAD4 genome

AF:

0.0631

AC:

9601

AN:

152152

Hom.:

616

Cov.:

AF XY:

0.0602

AC XY:

4482

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.0295

Gnomad4 ASJ

AF:

0.0153

Gnomad4 EAS

AF:

0.00639

Gnomad4 SAS

AF:

0.0381

Gnomad4 FIN

AF:

0.0127

Gnomad4 NFE

AF:

0.0258

Gnomad4 OTH

AF:

0.0477

Alfa

AF:

0.0449

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.6

DANN

Benign

0.41

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over