chr2-117921219-C-T

Variant names:

• chr2-117921219-C-T
• rs9284719
• NM_019044.5:c.1843-823G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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]

ENSG00000290590 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC93	NM_019044.5	c.1843-823G>A		intron_variant	Intron 23 of 23	ENST00000376300.7	NP_061917.3
CCDC93	XM_011511359.2	c.1840-823G>A		intron_variant	Intron 23 of 23		XP_011509661.2
CCDC93	XM_011511361.1	c.1555-823G>A		intron_variant	Intron 22 of 22		XP_011509663.1
CCDC93	XM_047444816.1	c.1444-823G>A		intron_variant	Intron 20 of 20		XP_047300772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC93	ENST00000376300.7	c.1843-823G>A		intron_variant	Intron 23 of 23	1	NM_019044.5	ENSP00000365477.2

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

African (AFR) AF: 0.487 AC: 19902 AN: 40864

American (AMR) AF: 0.299 AC: 4528 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1295 AN: 3466

East Asian (EAS) AF: 0.130 AC: 667 AN: 5122

South Asian (SAS) AF: 0.309 AC: 1472 AN: 4770

European-Finnish (FIN) AF: 0.220 AC: 2253 AN: 10230

Middle Eastern (MID) AF: 0.483 AC: 138 AN: 286

European-Non Finnish (NFE) AF: 0.347 AC: 23506 AN: 67770

Other (OTH) AF: 0.370 AC: 776 AN: 2096

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
PhyloP100		-0.54
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: rs9284719; hg19: chr2-118678795;