10-32680309-T-G

Variant names:

• chr10-32680309-T-G
• rs2247648
• NM_001395015.1:c.2123-5661T>G

Variant summary

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

The NM_001395015.1(CCDC7):​c.2123-5661T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,038 control chromosomes in the GnomAD database, including 11,313 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 0.34 (11313 hom., cov: 31)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 2 publications found

Genes affected

CCDC7 (HGNC:26533): (coiled-coil domain containing 7)

CCDC7 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395015.1. 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
	CCDC7	NM_001395015.1	MANE Select	c.2123-5661T>G		intron	N/A	NP_001381944.1
	CCDC7	NM_001321115.2		c.2123-5661T>G		intron	N/A	NP_001308044.1
	CCDC7	NM_001395233.1		c.1064-5661T>G		intron	N/A	NP_001382162.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC7	ENST00000639629.2	TSL:5 MANE Select	c.2123-5661T>G		intron	N/A	ENSP00000491655.1
	CCDC7	ENST00000302316.12	TSL:1	n.154-5661T>G		intron	N/A	ENSP00000303710.9
	CCDC7	ENST00000639290.1	TSL:1	n.685+4496T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51927 AN: 151920 Hom.: 11310 Cov.: 31

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.342 AC: 51930 AN: 152038 Hom.: 11313 Cov.: 31 AF XY: 0.338 AC XY: 25144 AN XY: 74310

African (AFR) AF: 0.0898 AC: 3730 AN: 41530

American (AMR) AF: 0.323 AC: 4933 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3468

East Asian (EAS) AF: 0.0880 AC: 455 AN: 5168

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4808

European-Finnish (FIN) AF: 0.485 AC: 5112 AN: 10534

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33488 AN: 67936

Other (OTH) AF: 0.356 AC: 752 AN: 2110

Alfa AF: 0.278 Hom.: 894

Bravo AF: 0.318

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.58
PhyloP100		-0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2247648; hg19: chr10-32969237;