rs708886

Positions:

• chr12-119520897-T-G

Variant summary

Our verdict is Benign. Variant got -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

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 (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC60	NM_178499.5	c.1040+705T>G		intron_variant		ENST00000327554.3
LOC105370027	XR_007063484.1	n.162+32651A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC60	ENST00000327554.3	c.1040+705T>G		intron_variant		1	NM_178499.5	P1
	ENST00000537366.5	n.235+32651A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.416

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.3
DANN	Benign	0.79

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: rs708886; hg19: chr12-119958702;