rs10508775

chr10-32575802-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+3909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,028 control chromosomes in the GnomAD database, including 11,460 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 (11460 hom., cov: 31)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

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 (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC7	NM_001395015.1	c.1454+3909G>A		intron_variant		ENST00000639629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC7	ENST00000639629.2	c.1454+3909G>A		intron_variant		5	NM_001395015.1	A2
CCDC7	ENST00000302316.12	c.56+7911G>A		intron_variant, NMD_transcript_variant		1
CCDC7	ENST00000639290.1	n.189+1276G>A		intron_variant, non_coding_transcript_variant		1
CCDC7	ENST00000375025.10	c.170-7232G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52372 AN: 151910 Hom.: 11457 Cov.: 31

Gnomad AFR AF: 0.0940

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.345 AC: 52375 AN: 152028 Hom.: 11460 Cov.: 31 AF XY: 0.341 AC XY: 25348 AN XY: 74300

Gnomad4 AFR AF: 0.0938

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.0879

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.360

Alfa AF: 0.460 Hom.: 33220

Bravo AF: 0.321

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.2
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508775; hg19: chr10-32864730;