rs1553009

chr7-45869395-G-A

Variant summary

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

The NM_001395235.1(CCDC201):c.19-2901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,212 control chromosomes in the GnomAD database, including 2,165 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 0.16 (2165 hom., cov: 32)
• Consequence: CCDC201 NM_001395235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC201	NM_001395235.1	c.19-2901C>T		intron_variant		ENST00000636578.2
CCDC201	XM_047419863.1	c.271-2087C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC201	ENST00000636578.2	c.19-2901C>T		intron_variant		5	NM_001395235.1	P1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23768 AN: 152094 Hom.: 2164 Cov.: 32

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.156 AC: 23765 AN: 152212 Hom.: 2165 Cov.: 32 AF XY: 0.153 AC XY: 11373 AN XY: 74432

Gnomad4 AFR AF: 0.0819

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.183

Alfa AF: 0.191 Hom.: 6133

Bravo AF: 0.164

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553009; hg19: chr7-45908994;