rs9312960

chr5-203967-C-Achr5-203967-C-T

Variant summary

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

The NM_145265.3(CCDC127):c.*1330G>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 0.335 in 152,044 control chromosomes in the GnomAD database, including 10,264 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 0.34 (10263 hom., cov: 33)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: CCDC127 NM_145265.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

CCDC127 (HGNC:30520): (coiled-coil domain containing 127) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC127	NM_145265.3	c.*1330G>T		3_prime_UTR_variant	3/3	ENST00000296824.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC127	ENST00000296824.4	c.*1330G>T		3_prime_UTR_variant	3/3	1	NM_145265.3	P1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50925 AN: 151890 Hom.: 10236 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0570

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.306 AC: 11 AN: 36 Hom.: 1 Cov.: 0 AF XY: 0.292 AC XY: 7 AN XY: 24

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.335 AC: 50998 AN: 152008 Hom.: 10263 Cov.: 33 AF XY: 0.331 AC XY: 24627 AN XY: 74308

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.0565

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.330

Alfa AF: 0.250 Hom.: 8543

Bravo AF: 0.352

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.48

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: rs9312960; hg19: chr5-204082;