chr7-45864208-C-T

Position:

• chr7-45864208-C-T

Variant summary

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

The NM_001395235.1(CCDC201):​c.478-1037G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0676 in 152,164 control chromosomes in the GnomAD database, including 580 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 0.068 (580 hom., cov: 32)
• Consequence: CCDC201 NM_001395235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

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 = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC201	NM_001395235.1	c.478-1037G>A		intron_variant		ENST00000636578.2	NP_001382164.1
CCDC201	XM_047419863.1	c.928-1037G>A		intron_variant			XP_047275819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC201	ENST00000636578.2	c.478-1037G>A		intron_variant		5	NM_001395235.1	ENSP00000489712.1

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10273 AN: 152046 Hom.: 578 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0676 AC: 10292 AN: 152164 Hom.: 580 Cov.: 32 AF XY: 0.0683 AC XY: 5079 AN XY: 74386

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0392

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.0614

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0308 Hom.: 35

Bravo AF: 0.0713

Asia WGS AF: 0.0920 AC: 320 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	0.13
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6956740; hg19: chr7-45903807;