chr2-117921219-C-T

Position:

• chr2-117921219-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019044.5(CCDC93):​c.1843-823G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 150,656 control chromosomes in the GnomAD database, including 10,801 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 0.36 (10801 hom., cov: 28)
• Consequence: CCDC93 NM_019044.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

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]

ENSG00000290590 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC93	NM_019044.5	c.1843-823G>A		intron_variant		ENST00000376300.7	NP_061917.3
CCDC93	XM_011511359.2	c.1840-823G>A		intron_variant			XP_011509661.2
CCDC93	XM_011511361.1	c.1555-823G>A		intron_variant			XP_011509663.1
CCDC93	XM_047444816.1	c.1444-823G>A		intron_variant			XP_047300772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC93	ENST00000376300.7	c.1843-823G>A		intron_variant		1	NM_019044.5	ENSP00000365477.2
ENSG00000290590	ENST00000434708.1	n.282-441C>T		intron_variant		1
CCDC93	ENST00000319432.9	c.1840-823G>A		intron_variant		5		ENSP00000324135.5
CCDC93	ENST00000437999.5	n.*483-823G>A		intron_variant		3		ENSP00000392989.1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 54851 AN: 150546 Hom.: 10785 Cov.: 28

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.374

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 54897 AN: 150656 Hom.: 10801 Cov.: 28 AF XY: 0.359 AC XY: 26365 AN XY: 73502

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.370

Alfa AF: 0.203 Hom.: 400

Bravo AF: 0.372

Asia WGS AF: 0.251 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs9284719; hg19: chr2-118678795;