rs12217414

Variant names:

• chr10-32876494-G-A
• rs12217414
• ENST00000302316.12:n.*1882G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-32876494-G-A
• chr10-32876494-G-C

Variant summary

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

The ENST00000302316.12(CCDC7):​n.*1882G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 1,115,690 control chromosomes in the GnomAD database, including 16,078 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 (1746 hom., cov: 32)
  • Exomes 𝑓: 0.17 (14332 hom.)
• Consequence: CCDC7 ENST00000302316.12 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.*101G>A		3_prime_UTR_variant	Exon 43 of 44	ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.*101G>A		3_prime_UTR_variant	Exon 43 of 44	5	NM_001395015.1	ENSP00000491655.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20907 AN: 151814 Hom.: 1748 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.170 AC: 163860 AN: 963756 Hom.: 14332 Cov.: 12 AF XY: 0.170 AC XY: 84501 AN XY: 497614

African (AFR) AF: 0.0400 AC: 889 AN: 22238

American (AMR) AF: 0.193 AC: 6630 AN: 34296

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 4339 AN: 22004

East Asian (EAS) AF: 0.251 AC: 9012 AN: 35846

South Asian (SAS) AF: 0.167 AC: 11599 AN: 69630

European-Finnish (FIN) AF: 0.146 AC: 7359 AN: 50530

Middle Eastern (MID) AF: 0.184 AC: 880 AN: 4776

European-Non Finnish (NFE) AF: 0.170 AC: 115492 AN: 681124

Other (OTH) AF: 0.177 AC: 7660 AN: 43312

GnomAD4 genome AF: 0.138 AC: 20910 AN: 151934 Hom.: 1746 Cov.: 32 AF XY: 0.138 AC XY: 10256 AN XY: 74242

African (AFR) AF: 0.0451 AC: 1870 AN: 41492

American (AMR) AF: 0.178 AC: 2709 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1273 AN: 5140

South Asian (SAS) AF: 0.167 AC: 804 AN: 4816

European-Finnish (FIN) AF: 0.155 AC: 1630 AN: 10550

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11353 AN: 67934

Other (OTH) AF: 0.169 AC: 357 AN: 2112

Alfa AF: 0.157 Hom.: 412

Bravo AF: 0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.75
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs12217414; hg19: chr10-33165422; COSMIC: COSV56542244;