rs10228265

Positions:

• chr7-45869316-A-G
• chr7-45869316-A-T

Variant summary

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

The NM_001395235.1(CCDC201):​c.19-2822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,100 control chromosomes in the GnomAD database, including 8,700 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 (8700 hom., cov: 33)
• Consequence: CCDC201 NM_001395235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

CCDC201 (HGNC:54081): (coiled-coil domain containing 201)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC201	NM_001395235.1	c.19-2822T>C		intron_variant		ENST00000636578.2	NP_001382164.1
CCDC201	XM_047419863.1	c.271-2008T>C		intron_variant			XP_047275819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC201	ENST00000636578.2	c.19-2822T>C		intron_variant		5	NM_001395235.1	ENSP00000489712	P1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50929 AN: 151982 Hom.: 8689 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.335 AC: 50973 AN: 152100 Hom.: 8700 Cov.: 33 AF XY: 0.334 AC XY: 24809 AN XY: 74340

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.321

Alfa AF: 0.307 Hom.: 7591

Bravo AF: 0.338

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
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: rs10228265; hg19: chr7-45908915;