chr10-59875036-C-A

Variant names:

• chr10-59875036-C-A
• rs1624715
• NM_005436.5:c.304-22334G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005436.5(CCDC6):​c.304-22334G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,196 control chromosomes in the GnomAD database, including 44,257 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 0.76 (44257 hom., cov: 33)
• Consequence: CCDC6 NM_005436.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 2 publications found

Genes affected

CCDC6 (HGNC:18782): (coiled-coil domain containing 6) This gene encodes a coiled-coil domain-containing protein. The encoded protein is ubiquitously expressed and may function as a tumor suppressor. A chromosomal rearrangement resulting in the expression of a fusion gene containing a portion of this gene and the intracellular kinase-encoding domain of the ret proto-oncogene is the cause of thyroid papillary carcinoma.[provided by RefSeq, Sep 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC6	NM_005436.5	c.304-22334G>T		intron_variant	Intron 1 of 8	ENST00000263102.7	NP_005427.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC6	ENST00000263102.7	c.304-22334G>T		intron_variant	Intron 1 of 8	1	NM_005436.5	ENSP00000263102.6

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115619 AN: 152078 Hom.: 44204 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.760 AC: 115733 AN: 152196 Hom.: 44257 Cov.: 33 AF XY: 0.765 AC XY: 56925 AN XY: 74424

African (AFR) AF: 0.791 AC: 32854 AN: 41516

American (AMR) AF: 0.797 AC: 12181 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2607 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4642 AN: 5180

South Asian (SAS) AF: 0.739 AC: 3573 AN: 4832

European-Finnish (FIN) AF: 0.808 AC: 8563 AN: 10604

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48832 AN: 67986

Other (OTH) AF: 0.742 AC: 1569 AN: 2114

Alfa AF: 0.687 Hom.: 2096

Bravo AF: 0.777

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.13
DANN	Benign	0.66
PhyloP100		-0.44
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: rs1624715; hg19: chr10-61634794;