rs12266925

chr10-32567517-A-G

Variant summary

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

The NM_001395015.1(CCDC7):c.1198-153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,230 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 32)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC7	NM_001395015.1	c.1198-153A>G		intron_variant		ENST00000639629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC7	ENST00000639629.2	c.1198-153A>G		intron_variant		5	NM_001395015.1	A2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15971 AN: 152112 Hom.: 1036 Cov.: 32

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.105 AC: 15988 AN: 152230 Hom.: 1040 Cov.: 32 AF XY: 0.110 AC XY: 8207 AN XY: 74422

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0776

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0996

Gnomad4 NFE AF: 0.0830

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.0876 Hom.: 481

Bravo AF: 0.109

Asia WGS AF: 0.215 AC: 747 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.41
Dann	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12266925; hg19: chr10-32856445;