rs2990962

Positions:

• chr10-32574659-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.1454+2766G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 355,794 control chromosomes in the GnomAD database, including 4,801 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 (1760 hom., cov: 32)
  • Exomes 𝑓: 0.17 (3041 hom.)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC7	NM_001395015.1	c.1454+2766G>A		intron_variant		ENST00000639629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC7	ENST00000639629.2	c.1454+2766G>A		intron_variant		5	NM_001395015.1	A2
CCDC7	ENST00000302316.12	c.56+6768G>A		intron_variant, NMD_transcript_variant		1
CCDC7	ENST00000639290.1	n.189+133G>A		intron_variant, non_coding_transcript_variant		1
CCDC7	ENST00000375025.10	c.169+6768G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21008 AN: 151960 Hom.: 1761 Cov.: 32

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.167 AC: 34030 AN: 203716 Hom.: 3041 AF XY: 0.168 AC XY: 17188 AN XY: 102488

Gnomad4 AFR exome AF: 0.0424

Gnomad4 AMR exome AF: 0.197

Gnomad4 ASJ exome AF: 0.196

Gnomad4 EAS exome AF: 0.258

Gnomad4 SAS exome AF: 0.177

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.166

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.138 AC: 21010 AN: 152078 Hom.: 1760 Cov.: 32 AF XY: 0.139 AC XY: 10315 AN XY: 74340

Gnomad4 AFR AF: 0.0454

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.171

Alfa AF: 0.162 Hom.: 875

Bravo AF: 0.137

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2990962; hg19: chr10-32863587;