rs2201638

Variant names:

• chr7-45883311-G-A
• rs2201638
• XM_047419863.1:c.270+1592C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047419863.1(CCDC201):​c.270+1592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 152,144 control chromosomes in the GnomAD database, including 933 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 0.082 (933 hom., cov: 32)
• Consequence: CCDC201 XM_047419863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12480 AN: 152026 Hom.: 927 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.0651

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0823 AC: 12515 AN: 152144 Hom.: 933 Cov.: 32 AF XY: 0.0837 AC XY: 6222 AN XY: 74380

African (AFR) AF: 0.195 AC: 8098 AN: 41462

American (AMR) AF: 0.0425 AC: 649 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3470

East Asian (EAS) AF: 0.0651 AC: 337 AN: 5180

South Asian (SAS) AF: 0.119 AC: 573 AN: 4822

European-Finnish (FIN) AF: 0.0463 AC: 490 AN: 10594

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0295 AC: 2009 AN: 68012

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0601 Hom.: 131

Bravo AF: 0.0855

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.34
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2201638; hg19: chr7-45922910;