10-32680309-T-G

Position:

• chr10-32680309-T-G

Variant summary

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

The NM_001395015.1(CCDC7):​c.2123-5661T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,038 control chromosomes in the GnomAD database, including 11,313 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 0.34 (11313 hom., cov: 31)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.2123-5661T>G		intron_variant		ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.2123-5661T>G		intron_variant		5	NM_001395015.1	ENSP00000491655	A2
CCDC7	ENST00000302316.12	c.156-5661T>G		intron_variant, NMD_transcript_variant		1		ENSP00000303710
CCDC7	ENST00000639290.1	n.685+4496T>G		intron_variant, non_coding_transcript_variant		1
CCDC7	ENST00000375025.10	c.*327-5661T>G		intron_variant, NMD_transcript_variant		2		ENSP00000364165

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51927 AN: 151920 Hom.: 11310 Cov.: 31

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.342 AC: 51930 AN: 152038 Hom.: 11313 Cov.: 31 AF XY: 0.338 AC XY: 25144 AN XY: 74310

Gnomad4 AFR AF: 0.0898

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.0880

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.356

Alfa AF: 0.289 Hom.: 888

Bravo AF: 0.318

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2247648; hg19: chr10-32969237;