10-32582877-T-G

Variant names:

• chr10-32582877-T-G
• rs3006739
• NM_001395015.1:c.1455-157T>G

Variant summary

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

The NM_001395015.1(CCDC7):​c.1455-157T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,120 control chromosomes in the GnomAD database, including 1,750 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 (1750 hom., cov: 31)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.1455-157T>G		intron_variant	Intron 17 of 43	ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.1455-157T>G		intron_variant	Intron 17 of 43	5	NM_001395015.1	ENSP00000491655.1
CCDC7	ENST00000302316.12	n.54+14986T>G		intron_variant	Intron 1 of 20	1		ENSP00000303710.9
CCDC7	ENST00000639290.1	n.190-157T>G		intron_variant	Intron 3 of 22	1
CCDC7	ENST00000375025.10	n.169-157T>G		intron_variant	Intron 1 of 22	2		ENSP00000364165.6

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21002 AN: 152000 Hom.: 1751 Cov.: 31

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.138 AC: 21004 AN: 152120 Hom.: 1750 Cov.: 31 AF XY: 0.139 AC XY: 10310 AN XY: 74344

Gnomad4 AFR AF: 0.0454

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.171

Alfa AF: 0.0733 Hom.: 87

Bravo AF: 0.137

Asia WGS AF: 0.209 AC: 722 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3006739; hg19: chr10-32871805;