rs2173035

Positions:

• chr7-45861950-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.*1135C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,284 control chromosomes in the GnomAD database, including 740 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 0.074 (740 hom., cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCDC201 NM_001395235.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC201	NM_001395235.1	c.*1135C>T		3_prime_UTR_variant	3/3	ENST00000636578.2	NP_001382164.1
CCDC201	XM_047419863.1	c.*1135C>T		3_prime_UTR_variant	4/4		XP_047275819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC201	ENST00000636578.2	c.*1135C>T		3_prime_UTR_variant	3/3	5	NM_001395235.1	ENSP00000489712	P1

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11323 AN: 152166 Hom.: 738 Cov.: 34

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0207

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0607

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0745 AC: 11341 AN: 152284 Hom.: 740 Cov.: 34 AF XY: 0.0744 AC XY: 5544 AN XY: 74470

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0422

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.0625

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0207

Gnomad4 NFE AF: 0.0287

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0389 Hom.: 171

Bravo AF: 0.0793

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2173035; hg19: chr7-45901549;