12-119512562-T-C

Position:

• chr12-119512562-T-C

Variant summary

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

The NM_178499.5(CCDC60):​c.884-4061T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,088 control chromosomes in the GnomAD database, including 34,858 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 0.66 (34858 hom., cov: 32)
• Consequence: CCDC60 NM_178499.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

Genes affected

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

ENSG00000248636 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC60	NM_178499.5	c.884-4061T>C		intron_variant		ENST00000327554.3	NP_848594.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC60	ENST00000327554.3	c.884-4061T>C		intron_variant		1	NM_178499.5	ENSP00000333374.2

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100208 AN: 151972 Hom.: 34810 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.660 AC: 100314 AN: 152088 Hom.: 34858 Cov.: 32 AF XY: 0.664 AC XY: 49350 AN XY: 74328

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.621

Alfa AF: 0.587 Hom.: 14799

Bravo AF: 0.676

Asia WGS AF: 0.774 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.41
DANN	Benign	0.63

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: rs474932; hg19: chr12-119950367;