7-45873165-A-G

Position:

• chr7-45873165-A-G

Variant summary

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

The XM_047419863.1(CCDC201):​c.271-5857T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,310 control chromosomes in the GnomAD database, including 53,257 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 0.83 (53197 hom., cov: 31)
  • Exomes 𝑓: 0.79 (60 hom.)
• Consequence: CCDC201 XM_047419863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

Genes affected

CCDC201 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC201	XM_047419863.1	c.271-5857T>C		intron_variant			XP_047275819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126371 AN: 152010 Hom.: 53144 Cov.: 31

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.829

GnomAD4 exome AF: 0.786 AC: 143 AN: 182 Hom.: 60 AF XY: 0.764 AC XY: 113 AN XY: 148

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.785

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.831 AC: 126485 AN: 152128 Hom.: 53197 Cov.: 31 AF XY: 0.832 AC XY: 61889 AN XY: 74358

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.827

Alfa AF: 0.767 Hom.: 57134

Bravo AF: 0.839

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10241749; hg19: chr7-45912764;