rs11064768

Positions:

• chr12-119380704-A-G

Variant summary

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

The ENST00000327554.3(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 ENST00000327554.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

Genes affected

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC60	NM_178499.5	c.90+45438A>G		intron_variant		ENST00000327554.3	NP_848594.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC60	ENST00000327554.3	c.90+45438A>G		intron_variant		1	NM_178499.5	ENSP00000333374	P1

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

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.0647

Alfa AF: 0.0786 Hom.: 805

Bravo AF: 0.0541

Asia WGS AF: 0.0340 AC: 121 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	1.0
DANN	Benign	0.61

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: rs11064768; hg19: chr12-119818509;