18-54933466-T-C

Variant names:

• chr18-54933466-T-C
• rs9964104
• NM_025214.3:c.600+1354A>G

Variant summary

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

The NM_025214.3(CCDC68):​c.600+1354A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,052 control chromosomes in the GnomAD database, including 11,388 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 0.38 (11388 hom., cov: 32)
• Consequence: CCDC68 NM_025214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 1 publications found

Genes affected

CCDC68 (HGNC:24350): (coiled-coil domain containing 68) Involved in microtubule anchoring at centrosome and protein localization. Located in centriole. Part of centriolar subdistal appendage. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025214.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC68	NM_025214.3	MANE Select	c.600+1354A>G		intron	N/A	NP_079490.1	Q9H2F9
	CCDC68	NM_001143829.2		c.600+1354A>G		intron	N/A	NP_001137301.1	Q9H2F9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC68	ENST00000591504.6	TSL:1 MANE Select	c.600+1354A>G		intron	N/A	ENSP00000466690.1	Q9H2F9
	CCDC68	ENST00000432185.5	TSL:1	c.600+1354A>G		intron	N/A	ENSP00000413406.1	Q9H2F9
	CCDC68	ENST00000337363.8	TSL:2	c.600+1354A>G		intron	N/A	ENSP00000337209.3	Q9H2F9

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58210 AN: 151934 Hom.: 11381 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.383 AC: 58242 AN: 152052 Hom.: 11388 Cov.: 32 AF XY: 0.388 AC XY: 28838 AN XY: 74348

African (AFR) AF: 0.345 AC: 14307 AN: 41454

American (AMR) AF: 0.439 AC: 6711 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3028 AN: 5174

South Asian (SAS) AF: 0.377 AC: 1822 AN: 4828

European-Finnish (FIN) AF: 0.448 AC: 4731 AN: 10556

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25309 AN: 67970

Other (OTH) AF: 0.373 AC: 787 AN: 2112

Alfa AF: 0.372 Hom.: 5619

Bravo AF: 0.388

Asia WGS AF: 0.456 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.66
DANN	Benign	0.42
PhyloP100		-0.38
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: rs9964104; hg19: chr18-52600697;