rs1335995

chr10-32741180-A-Gchr10-32741180-A-T

Variant summary

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

The NM_001395015.1(CCDC7):c.2905+11723A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 152,212 control chromosomes in the GnomAD database, including 872 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 0.085 (872 hom., cov: 32)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

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=-0.99).
• 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.2905+11723A>G		intron_variant		ENST00000639629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC7	ENST00000639629.2	c.2905+11723A>G		intron_variant		5	NM_001395015.1	A2

Frequencies

GnomAD3 genomes AF: 0.0855 AC: 12998 AN: 152092 Hom.: 868 Cov.: 32

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.0929

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0855 AC: 13008 AN: 152212 Hom.: 872 Cov.: 32 AF XY: 0.0922 AC XY: 6862 AN XY: 74434

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0773

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0994

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0341 Hom.: 17

Bravo AF: 0.0867

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.45
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335995; hg19: chr10-33030108;