rs708886

Variant names:

• chr12-119520897-T-G
• rs708886
• NM_178499.5:c.1040+705T>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.1040+705T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,952 control chromosomes in the GnomAD database, including 16,800 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 0.46 (16800 hom., cov: 32)
• Consequence: CCDC60 NM_178499.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 2 publications found

Genes affected

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

ENSG00000248636 (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 (AFR) allele frequency at 95% confidence interval = 0.599 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC60	NM_178499.5	MANE Select	c.1040+705T>G		intron	N/A	NP_848594.2
	PRKAB1-AS1	NR_188489.1		n.885+32651A>C		intron	N/A
	PRKAB1-AS1	NR_188490.1		n.283+32651A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC60	ENST00000327554.3	TSL:1 MANE Select	c.1040+705T>G		intron	N/A	ENSP00000333374.2
	ENSG00000248636	ENST00000509470.2	TSL:1	n.418+32651A>C		intron	N/A
	ENSG00000248636	ENST00000535511.6	TSL:3	n.885+32651A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70021 AN: 151834 Hom.: 16772 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.461 AC: 70104 AN: 151952 Hom.: 16800 Cov.: 32 AF XY: 0.462 AC XY: 34324 AN XY: 74298

African (AFR) AF: 0.606 AC: 25080 AN: 41420

American (AMR) AF: 0.408 AC: 6228 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3472

East Asian (EAS) AF: 0.372 AC: 1916 AN: 5156

South Asian (SAS) AF: 0.323 AC: 1556 AN: 4822

European-Finnish (FIN) AF: 0.456 AC: 4812 AN: 10560

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27837 AN: 67950

Other (OTH) AF: 0.416 AC: 876 AN: 2104

Alfa AF: 0.438 Hom.: 1860

Bravo AF: 0.467

Asia WGS AF: 0.348 AC: 1210 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	5.3
DANN	Benign	0.79
PhyloP100		-0.083
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: rs708886; hg19: chr12-119958702;