12-119472154-AC-A

Position:

• chr12-119472154-AC-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_178499.5(CCDC60):​c.333del​(p.Leu112TyrfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000615 in 1,613,968 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.00060 (1 hom., cov: 31)
  • Exomes 𝑓: 0.00062 (2 hom.)
• Consequence: CCDC60 NM_178499.5 frameshift
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.222

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 12-119472154-AC-A is Benign according to our data. Variant chr12-119472154-AC-A is described in ClinVar as [Likely_benign]. Clinvar id is 3025112.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC60	NM_178499.5	c.333del	p.Leu112TyrfsTer2	frameshift_variant	3/14	ENST00000327554.3
LOC105370027	XR_007063484.1	n.162+81393del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC60	ENST00000327554.3	c.333del	p.Leu112TyrfsTer2	frameshift_variant	3/14	1	NM_178499.5	P1
	ENST00000537366.5	n.236-69725del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.000604 AC: 92 AN: 152222 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.000823

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.000724 AC: 182 AN: 251306 Hom.: 0 AF XY: 0.000722 AC XY: 98 AN XY: 135816

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.00133

Gnomad ASJ exome AF: 0.000198

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000654

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000897

Gnomad OTH exome AF: 0.00180

GnomAD4 exome AF: 0.000616 AC: 901 AN: 1461628 Hom.: 2 Cov.: 31 AF XY: 0.000641 AC XY: 466 AN XY: 727134

Gnomad4 AFR exome AF: 0.000209

Gnomad4 AMR exome AF: 0.00137

Gnomad4 ASJ exome AF: 0.0000765

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000765

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000578

Gnomad4 OTH exome AF: 0.00113

GnomAD4 genome AF: 0.000604 AC: 92 AN: 152340 Hom.: 1 Cov.: 31 AF XY: 0.000617 AC XY: 46 AN XY: 74502

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000823

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.000215 Hom.: 0

Bravo AF: 0.000703

EpiCase AF: 0.00120

EpiControl AF: 0.00148

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

CCDC60: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs559574757; hg19: chr12-119909959;