7-45859760-C-T

Variant names:

• chr7-45859760-C-T
• rs6972219
• ENST00000780168.1:n.570+225C>T

Variant summary

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

The ENST00000780168.1(ENSG00000301608):​n.570+225C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 152,220 control chromosomes in the GnomAD database, including 552 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 0.067 (552 hom., cov: 33)
• Consequence: ENSG00000301608 ENST00000780168.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37
• Publications: 4 publications found

Genes affected

ENSG00000301608 (HGNC:):

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780168.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC201	NM_001395235.1	MANE Select	c.*3325G>A		downstream_gene	N/A	NP_001382164.1	A0A1B0GTI1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301608	ENST00000780168.1		n.570+225C>T		intron	N/A
	CCDC201	ENST00000636578.2	TSL:5 MANE Select	c.*3325G>A		downstream_gene	N/A	ENSP00000489712.1	A0A1B0GTI1

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10256 AN: 152102 Hom.: 550 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0303

Gnomad OTH AF: 0.0576

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

GnomAD4 genome AF: 0.0675 AC: 10271 AN: 152220 Hom.: 552 Cov.: 33 AF XY: 0.0681 AC XY: 5070 AN XY: 74418

African (AFR) AF: 0.148 AC: 6148 AN: 41512

American (AMR) AF: 0.0392 AC: 599 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0488 AC: 169 AN: 3466

East Asian (EAS) AF: 0.0627 AC: 325 AN: 5184

South Asian (SAS) AF: 0.119 AC: 573 AN: 4816

European-Finnish (FIN) AF: 0.0208 AC: 220 AN: 10602

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

European-Non Finnish (NFE) AF: 0.0303 AC: 2060 AN: 68034

Other (OTH) AF: 0.0570 AC: 120 AN: 2106

Alfa AF: 0.0359 Hom.: 109

Bravo AF: 0.0708

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.41
PhyloP100		-3.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6972219;

hg19: chr7-45899359;