rs11064768

Variant names:

• chr12-119380704-A-G
• rs11064768
• NM_178499.5:c.90+45438A>G

Variant summary

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

The NM_178499.5(CCDC60):​c.90+45438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,302 control chromosomes in the GnomAD database, including 321 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 0.056 (321 hom., cov: 33)
• Consequence: CCDC60 NM_178499.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 12 publications found

Genes affected

CCDC60 (HGNC:28610): (coiled-coil domain containing 60)

PRKAB1-AS1 (HGNC:58183):

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 (SAS) allele frequency at 95% confidence interval = 0.0877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178499.5. 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
	CCDC60	NM_178499.5	MANE Select	c.90+45438A>G		intron	N/A	NP_848594.2	Q8IWA6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC60	ENST00000327554.3	TSL:1 MANE Select	c.90+45438A>G		intron	N/A	ENSP00000333374.2	Q8IWA6
	CCDC60	ENST00000546345.5	TSL:1	n.240+45438A>G		intron	N/A
	CCDC60	ENST00000886826.1		c.90+45438A>G		intron	N/A	ENSP00000556885.1

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8604 AN: 152184 Hom.: 322 Cov.: 33

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0565 AC: 8603 AN: 152302 Hom.: 321 Cov.: 33 AF XY: 0.0540 AC XY: 4024 AN XY: 74478

African (AFR) AF: 0.0185 AC: 768 AN: 41588

American (AMR) AF: 0.0509 AC: 779 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0949 AC: 458 AN: 4826

European-Finnish (FIN) AF: 0.0363 AC: 385 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0826 AC: 5619 AN: 68014

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0729 Hom.: 1155

Bravo AF: 0.0541

Asia WGS AF: 0.0340 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		-0.67
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: rs11064768; hg19: chr12-119818509;