chr7-45872865-C-G

Position:

• chr7-45872865-C-G

Variant summary

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

The NM_001395235.1(CCDC201):​c.18+125G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,820 control chromosomes in the GnomAD database, including 6,220 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 0.28 (6189 hom., cov: 33)
  • Exomes 𝑓: 0.26 (31 hom.)
• Consequence: CCDC201 NM_001395235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC201	NM_001395235.1	c.18+125G>C		intron_variant		ENST00000636578.2	NP_001382164.1
CCDC201	XM_047419863.1	c.271-5557G>C		intron_variant			XP_047275819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC201	ENST00000636578.2	c.18+125G>C		intron_variant		5	NM_001395235.1	ENSP00000489712	P1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42393 AN: 151988 Hom.: 6181 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.270

GnomAD4 exome AF: 0.256 AC: 183 AN: 714 Hom.: 31 AF XY: 0.257 AC XY: 136 AN XY: 530

Gnomad4 AFR exome AF: 0.357

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.556

Gnomad4 NFE exome AF: 0.257

Gnomad4 OTH exome AF: 0.0769

GnomAD4 genome AF: 0.279 AC: 42429 AN: 152106 Hom.: 6189 Cov.: 33 AF XY: 0.286 AC XY: 21262 AN XY: 74316

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.267

Alfa AF: 0.167 Hom.: 382

Bravo AF: 0.268

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35539615; hg19: chr7-45912464;