2-117951274-C-G

Variant names:

• chr2-117951274-C-G
• rs3771942
• NM_019044.5:c.1068+1099G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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	c.1068+1099G>C		intron_variant	Intron 13 of 23	ENST00000376300.7	NP_061917.3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87834 AN: 151914 Hom.: 25732 Cov.: 32

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.: 30 AF XY: 0.596 AC XY: 229272 AN XY: 384644

African (AFR) AF: 0.621 AC: 9810 AN: 15786

American (AMR) AF: 0.453 AC: 446 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 2760 AN: 5150

East Asian (EAS) AF: 0.323 AC: 1172 AN: 3630

South Asian (SAS) AF: 0.577 AC: 9489 AN: 16458

European-Finnish (FIN) AF: 0.562 AC: 155 AN: 276

Middle Eastern (MID) AF: 0.550 AC: 891 AN: 1620

European-Non Finnish (NFE) AF: 0.598 AC: 455361 AN: 761736

Other (OTH) AF: 0.579 AC: 15802 AN: 27290

GnomAD4 genome AF: 0.578 AC: 87926 AN: 152030 Hom.: 25764 Cov.: 32 AF XY: 0.579 AC XY: 43033 AN XY: 74316

African (AFR) AF: 0.611 AC: 25351 AN: 41468

American (AMR) AF: 0.527 AC: 8047 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1674 AN: 5154

South Asian (SAS) AF: 0.587 AC: 2829 AN: 4816

European-Finnish (FIN) AF: 0.586 AC: 6185 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39965 AN: 67982

Other (OTH) AF: 0.568 AC: 1198 AN: 2108

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
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3771942; hg19: chr2-118708850;