NM_001395015.1:c.1454+3909G>A

Variant names:

• chr10-32575802-G-A
• rs10508775
• NM_001395015.1:c.1454+3909G>A

Variant summary

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

The NM_001395015.1(CCDC7):​c.1454+3909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,028 control chromosomes in the GnomAD database, including 11,460 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 (11460 hom., cov: 31)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.1454+3909G>A		intron_variant	Intron 17 of 43	ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.1454+3909G>A		intron_variant	Intron 17 of 43	5	NM_001395015.1	ENSP00000491655.1
CCDC7	ENST00000302316.12	n.54+7911G>A		intron_variant	Intron 1 of 20	1		ENSP00000303710.9
CCDC7	ENST00000639290.1	n.189+1276G>A		intron_variant	Intron 3 of 22	1
CCDC7	ENST00000375025.10	n.169-7232G>A		intron_variant	Intron 1 of 22	2		ENSP00000364165.6

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52372 AN: 151910 Hom.: 11457 Cov.: 31

Gnomad AFR AF: 0.0940

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.485

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: 0.345 AC: 52375 AN: 152028 Hom.: 11460 Cov.: 31 AF XY: 0.341 AC XY: 25348 AN XY: 74300

African (AFR) AF: 0.0938 AC: 3891 AN: 41490

American (AMR) AF: 0.326 AC: 4973 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3468

East Asian (EAS) AF: 0.0879 AC: 455 AN: 5174

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4816

European-Finnish (FIN) AF: 0.485 AC: 5118 AN: 10556

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

European-Non Finnish (NFE) AF: 0.496 AC: 33672 AN: 67942

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

Alfa AF: 0.437 Hom.: 49317

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	-0.90
CADD	Benign	7.2
DANN	Benign	0.67
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs10508775; hg19: chr10-32864730;