rs12217414

chr10-32876494-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395015.1(CCDC7):c.*101G>A variant causes a 3 prime UTR 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 NM_001395015.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

Genes affected

CCDC7 (HGNC:26533): (coiled-coil domain containing 7)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCDC7	NM_001395015.1	c.*101G>A		3_prime_UTR_variant	43/44	ENST00000639629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC7	ENST00000639629.2	c.*101G>A		3_prime_UTR_variant	43/44	5	NM_001395015.1	A2

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

Gnomad4 AFR exome AF: 0.0400

Gnomad4 AMR exome AF: 0.193

Gnomad4 ASJ exome AF: 0.197

Gnomad4 EAS exome AF: 0.251

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.146

Gnomad4 NFE exome AF: 0.170

Gnomad4 OTH exome AF: 0.177

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

Gnomad4 AFR AF: 0.0451

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.169

Alfa AF: 0.160 Hom.: 411

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

Splicing

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

Publications

LitVar

Other links and lift over

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