10-32489182-G-T

Variant names:

• chr10-32489182-G-T
• rs953818
• NM_001395015.1:c.797-2740G>T

Variant summary

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

The NM_001395015.1(CCDC7):​c.797-2740G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,110 control chromosomes in the GnomAD database, including 11,464 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 (11464 hom., cov: 32)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.797-2740G>T		intron_variant	Intron 9 of 43	ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.797-2740G>T		intron_variant	Intron 9 of 43	5	NM_001395015.1	ENSP00000491655.1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52334 AN: 151992 Hom.: 11461 Cov.: 32

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.344 AC: 52337 AN: 152110 Hom.: 11464 Cov.: 32 AF XY: 0.341 AC XY: 25328 AN XY: 74336

African (AFR) AF: 0.0918 AC: 3811 AN: 41520

American (AMR) AF: 0.326 AC: 4978 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1594 AN: 3470

East Asian (EAS) AF: 0.0875 AC: 453 AN: 5176

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4826

European-Finnish (FIN) AF: 0.484 AC: 5113 AN: 10566

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33706 AN: 67962

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.307 Hom.: 979

Bravo AF: 0.321

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.80
PhyloP100		0.34
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: rs953818; hg19: chr10-32778110;