chr10-32666177-G-A

Variant names:

• chr10-32666177-G-A
• rs7899442
• NM_001395015.1:c.2122+2016G>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.2122+2016G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 145,876 control chromosomes in the GnomAD database, including 11,795 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 0.40 (11795 hom., cov: 26)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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.2122+2016G>A		intron	N/A	NP_001381944.1
	CCDC7	NM_001321115.2		c.2122+2016G>A		intron	N/A	NP_001308044.1
	CCDC7	NM_001395233.1		c.1064-19793G>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.2122+2016G>A		intron	N/A	ENSP00000491655.1
	CCDC7	ENST00000302316.12	TSL:1	n.154-19793G>A		intron	N/A	ENSP00000303710.9
	CCDC7	ENST00000639290.1	TSL:1	n.537-9488G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 58349 AN: 145800 Hom.: 11787 Cov.: 26

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.400 AC: 58377 AN: 145876 Hom.: 11795 Cov.: 26 AF XY: 0.408 AC XY: 28848 AN XY: 70764

African (AFR) AF: 0.392 AC: 15590 AN: 39758

American (AMR) AF: 0.510 AC: 7462 AN: 14642

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1463 AN: 3440

East Asian (EAS) AF: 0.586 AC: 2935 AN: 5006

South Asian (SAS) AF: 0.549 AC: 2559 AN: 4664

European-Finnish (FIN) AF: 0.370 AC: 3273 AN: 8840

Middle Eastern (MID) AF: 0.415 AC: 118 AN: 284

European-Non Finnish (NFE) AF: 0.357 AC: 23682 AN: 66326

Other (OTH) AF: 0.416 AC: 839 AN: 2018

Alfa AF: 0.375 Hom.: 5821

Bravo AF: 0.406

Asia WGS AF: 0.597 AC: 2062 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.33
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7899442; hg19: chr10-32955105;