rs2990962

Variant names:

• chr10-32574659-G-A
• rs2990962
• NM_001395015.1:c.1454+2766G>A

Variant summary

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

The ENST00000639629.2(CCDC7):​c.1454+2766G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 355,794 control chromosomes in the GnomAD database, including 4,801 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 0.14 (1760 hom., cov: 32)
  • Exomes 𝑓: 0.17 (3041 hom.)
• Consequence: CCDC7 ENST00000639629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639629.2. 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.1454+2766G>A		intron	N/A	NP_001381944.1
	CCDC7	NM_001321115.2		c.1454+2766G>A		intron	N/A	NP_001308044.1
	CCDC7	NM_001395233.1		c.716+2766G>A		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.1454+2766G>A		intron	N/A	ENSP00000491655.1
	CCDC7	ENST00000302316.12	TSL:1	n.54+6768G>A		intron	N/A	ENSP00000303710.9
	CCDC7	ENST00000639290.1	TSL:1	n.189+133G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21008 AN: 151960 Hom.: 1761 Cov.: 32

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.167 AC: 34030 AN: 203716 Hom.: 3041 AF XY: 0.168 AC XY: 17188 AN XY: 102488

African (AFR) AF: 0.0424 AC: 196 AN: 4628

American (AMR) AF: 0.197 AC: 658 AN: 3334

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 859 AN: 4376

East Asian (EAS) AF: 0.258 AC: 2555 AN: 9906

South Asian (SAS) AF: 0.177 AC: 737 AN: 4166

European-Finnish (FIN) AF: 0.143 AC: 3015 AN: 21110

Middle Eastern (MID) AF: 0.209 AC: 141 AN: 674

European-Non Finnish (NFE) AF: 0.166 AC: 24210 AN: 145844

Other (OTH) AF: 0.171 AC: 1659 AN: 9678

GnomAD4 genome AF: 0.138 AC: 21010 AN: 152078 Hom.: 1760 Cov.: 32 AF XY: 0.139 AC XY: 10315 AN XY: 74340

African (AFR) AF: 0.0454 AC: 1884 AN: 41516

American (AMR) AF: 0.179 AC: 2742 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1305 AN: 5176

South Asian (SAS) AF: 0.170 AC: 819 AN: 4818

European-Finnish (FIN) AF: 0.155 AC: 1636 AN: 10560

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11351 AN: 67948

Other (OTH) AF: 0.171 AC: 360 AN: 2110

Alfa AF: 0.161 Hom.: 1017

Bravo AF: 0.137

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.52
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2990962; hg19: chr10-32863587;