chr7-45861950-G-A

Variant names:

• chr7-45861950-G-A
• rs2173035
• NM_001395235.1:c.*1135C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC201	NM_001395235.1	MANE Select	c.*1135C>T		3_prime_UTR	Exon 3 of 3	NP_001382164.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC201	ENST00000636578.2	TSL:5 MANE Select	c.*1135C>T		3_prime_UTR	Exon 3 of 3	ENSP00000489712.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.175 AC: 7271 AN: 41540

American (AMR) AF: 0.0422 AC: 646 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.0625 AC: 324 AN: 5180

South Asian (SAS) AF: 0.118 AC: 571 AN: 4826

European-Finnish (FIN) AF: 0.0207 AC: 220 AN: 10626

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

European-Non Finnish (NFE) AF: 0.0287 AC: 1955 AN: 68020

Other (OTH) AF: 0.0601 AC: 127 AN: 2114

Alfa AF: 0.0427 Hom.: 347

Bravo AF: 0.0793

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	-0.90
CADD	Benign	0.31
DANN	Benign	0.29
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2173035; hg19: chr7-45901549;