rs951342

Variant names:

• chr10-32739207-T-G
• rs951342
• NM_001395015.1:c.2905+9750T>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.2905+9750T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,074 control chromosomes in the GnomAD database, including 1,762 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 (1762 hom., cov: 32)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 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.2905+9750T>G		intron	N/A	NP_001381944.1
	CCDC7	NM_001321115.2		c.2905+9750T>G		intron	N/A	NP_001308044.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC7	ENST00000639629.2	TSL:5 MANE Select	c.2905+9750T>G		intron	N/A	ENSP00000491655.1
	CCDC7	ENST00000302316.12	TSL:1	n.*636+9750T>G		intron	N/A	ENSP00000303710.9
	CCDC7	ENST00000639290.1	TSL:1	n.1468+9750T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21039 AN: 151956 Hom.: 1763 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.138 AC: 21042 AN: 152074 Hom.: 1762 Cov.: 32 AF XY: 0.139 AC XY: 10318 AN XY: 74354

African (AFR) AF: 0.0453 AC: 1882 AN: 41540

American (AMR) AF: 0.179 AC: 2743 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1298 AN: 5164

South Asian (SAS) AF: 0.170 AC: 820 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1618 AN: 10544

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

European-Non Finnish (NFE) AF: 0.168 AC: 11406 AN: 67942

Other (OTH) AF: 0.171 AC: 361 AN: 2106

Alfa AF: 0.150 Hom.: 241

Bravo AF: 0.137

Asia WGS AF: 0.209 AC: 721 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.66
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs951342; hg19: chr10-33028135;