Genetic Variant CCDC93:c.1068+1099G>C (chr2-117951274-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019044.5(CCDC93):c.1068+1099G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 984,960 control chromosomes in the GnomAD database, including 173,812 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 0.58 ( 25764 hom., cov: 32)

Exomes 𝑓: 0.60 ( 148048 hom. )

Consequence

CCDC93
NM_019044.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.765

Variant links:

Genes affected

CCDC93 (HGNC:25611): (coiled-coil domain containing 93) Involved in Golgi to plasma membrane transport and endocytic recycling. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

CCDC93 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC93	NM_019044.5 link	c.1068+1099G>C		intron_variant	Intron 13 of 23	ENST00000376300.7	NP_061917.3	Q567U6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC93	ENST00000376300.7 link	c.1068+1099G>C	intron_variant	Intron 13 of 23	1	NM_019044.5	ENSP00000365477.2	Q567U6
CCDC93	ENST00000319432.9 link	c.1065+1099G>C	intron_variant	Intron 13 of 23	5		ENSP00000324135.5	F8W9X7
CCDC93	ENST00000488908.1 link	n.40+1099G>C	intron_variant	Intron 1 of 2	5
CCDC93	ENST00000460781.1 link	n.*215G>C	downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87834

AN:

151914

Hom.:

25732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.611

Gnomad AMI

AF:

0.707

Gnomad AMR

AF:

0.527

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.586

Gnomad FIN

AF:

0.586

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.588

Gnomad OTH

AF:

0.564

GnomAD4 exome

AF:

0.595

AC:

495886

AN:

832930

Hom.:

148048

Cov.:

AF XY:

0.596

AC XY:

229272

AN XY:

384644

show subpopulations

Gnomad4 AFR exome

AF:

0.621

Gnomad4 AMR exome

AF:

0.453

Gnomad4 ASJ exome

AF:

0.536

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.577

Gnomad4 FIN exome

AF:

0.562

Gnomad4 NFE exome

AF:

0.598

Gnomad4 OTH exome

AF:

0.579

GnomAD4 genome

AF:

0.578

AC:

87926

AN:

152030

Hom.:

25764

Cov.:

AF XY:

0.579

AC XY:

43033

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.611

Gnomad4 AMR

AF:

0.527

Gnomad4 ASJ

AF:

0.533

Gnomad4 EAS

AF:

0.325

Gnomad4 SAS

AF:

0.587

Gnomad4 FIN

AF:

0.586

Gnomad4 NFE

AF:

0.588

Gnomad4 OTH

AF:

0.568

Alfa

AF:

0.469

Hom.:

1289

Bravo

AF:

0.568

Asia WGS

AF:

0.495

AC:

1725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.042

DANN

Benign

0.47

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over