7-45869316-A-G

Variant names:

• chr7-45869316-A-G
• rs10228265
• NM_001395235.1:c.19-2822T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC201	NM_001395235.1	MANE Select	c.19-2822T>C		intron	N/A	NP_001382164.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC201	ENST00000636578.2	TSL:5 MANE Select	c.19-2822T>C		intron	N/A	ENSP00000489712.1

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

African (AFR) AF: 0.407 AC: 16894 AN: 41468

American (AMR) AF: 0.277 AC: 4245 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1870 AN: 5160

South Asian (SAS) AF: 0.280 AC: 1355 AN: 4832

European-Finnish (FIN) AF: 0.342 AC: 3615 AN: 10574

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20750 AN: 67976

Other (OTH) AF: 0.321 AC: 677 AN: 2110

Alfa AF: 0.311 Hom.: 10136

Bravo AF: 0.338

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.58
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs10228265; hg19: chr7-45908915;