rs7899442

chr10-32666177-G-Achr10-32666177-G-Cchr10-32666177-G-T

Variant summary

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

The NM_001395015.1(CCDC7):c.2122+2016G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 145,876 control chromosomes in the GnomAD database, including 11,795 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 0.40 (11795 hom., cov: 26)
• Consequence: CCDC7 NM_001395015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC7	NM_001395015.1	c.2122+2016G>A		intron_variant		ENST00000639629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC7	ENST00000639629.2	c.2122+2016G>A		intron_variant		5	NM_001395015.1	A2
CCDC7	ENST00000302316.12	c.156-19793G>A		intron_variant, NMD_transcript_variant		1
CCDC7	ENST00000639290.1	n.537-9488G>A		intron_variant, non_coding_transcript_variant		1
CCDC7	ENST00000375025.10	c.*327-19793G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.400 AC: 58349 AN: 145800 Hom.: 11787 Cov.: 26

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.400 AC: 58377 AN: 145876 Hom.: 11795 Cov.: 26 AF XY: 0.408 AC XY: 28848 AN XY: 70764

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.416

Alfa AF: 0.377 Hom.: 5259

Bravo AF: 0.406

Asia WGS AF: 0.597 AC: 2062 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.7
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7899442; hg19: chr10-32955105;