rs553588726

Variant names:

• chr16-722645-AGCTCT-A
• rs553588726
• NM_001378030.1:c.*28_*32delAGAGC

Your query was ambiguous. Multiple possible variants found:

• chr16-722645-AGCTCT-A
• chr16-722645-AGCTCT-AGCTCTGCTCT
• chr16-722645-AGCTCT-AGCTCTGCTCTGCTCT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001378030.1(CCDC78):​c.*28_*32delAGAGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000257 in 1,594,970 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000025 (0 hom.)
• Consequence: CCDC78 NM_001378030.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.833
• Publications: 0 publications found

Genes affected

CCDC78 (HGNC:14153): (coiled-coil domain containing 78) Involved in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation and skeletal muscle contraction. Located in several cellular components, including centriole; deuterosome; and sarcolemma. Implicated in centronuclear myopathy 4. [provided by Alliance of Genome Resources, Apr 2022]

ANTKMT (HGNC:14152): (adenine nucleotide translocase lysine methyltransferase) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 5 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378030.1. 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
	CCDC78	NM_001378030.1	MANE Select	c.*28_*32delAGAGC		3_prime_UTR	Exon 14 of 14	NP_001364959.1	H3BLT8
	CCDC78	NM_001031737.3		c.*120_*124delAGAGC		3_prime_UTR	Exon 14 of 14	NP_001026907.2	A2IDD5-1
	CCDC78	NM_001378031.1		c.*28_*32delAGAGC		3_prime_UTR	Exon 12 of 12	NP_001364960.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC78	ENST00000345165.10	TSL:5 MANE Select	c.*28_*32delAGAGC		3_prime_UTR	Exon 14 of 14	ENSP00000316851.5	H3BLT8
	CCDC78	ENST00000293889.10	TSL:1	c.*120_*124delAGAGC		3_prime_UTR	Exon 14 of 14	ENSP00000293889.6	A2IDD5-1
	CCDC78	ENST00000947033.1		c.*28_*32delAGAGC		3_prime_UTR	Exon 14 of 14	ENSP00000617092.1

Frequencies

GnomAD3 genomes AF: 0.0000329 AC: 5 AN: 151918 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000378 AC: 9 AN: 238024 AF XY: 0.0000230

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000117

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000110

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000909

Gnomad OTH exome AF: 0.000169

GnomAD4 exome AF: 0.0000249 AC: 36 AN: 1442934 Hom.: 0 AF XY: 0.0000279 AC XY: 20 AN XY: 717212

African (AFR) AF: 0.00 AC: 0 AN: 33226

American (AMR) AF: 0.000112 AC: 5 AN: 44524

Ashkenazi Jewish (ASJ) AF: 0.0000385 AC: 1 AN: 25984

East Asian (EAS) AF: 0.0000759 AC: 3 AN: 39516

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 85990

European-Finnish (FIN) AF: 0.0000240 AC: 1 AN: 41622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5738

European-Non Finnish (NFE) AF: 0.0000217 AC: 24 AN: 1106356

Other (OTH) AF: 0.0000167 AC: 1 AN: 59978

GnomAD4 genome AF: 0.0000329 AC: 5 AN: 152036 Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2 AN XY: 74314

African (AFR) AF: 0.0000241 AC: 1 AN: 41422

American (AMR) AF: 0.00 AC: 0 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 67970

Other (OTH) AF: 0.00 AC: 0 AN: 2112

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs553588726; hg19: chr16-772645;