rs1054174

chr5-204837-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.*460G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,994 control chromosomes in the GnomAD database, including 10,905 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 (10869 hom., cov: 33)
  • Exomes 𝑓: 0.23 (36 hom.)
• Consequence: CCDC127 NM_145265.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC127	NM_145265.3	c.*460G>A		3_prime_UTR_variant	3/3	ENST00000296824.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC127	ENST00000296824.4	c.*460G>A		3_prime_UTR_variant	3/3	1	NM_145265.3	P1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52089 AN: 151960 Hom.: 10837 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.337

GnomAD4 exome AF: 0.226 AC: 207 AN: 916 Hom.: 36 Cov.: 0 AF XY: 0.228 AC XY: 102 AN XY: 448

Gnomad4 AFR exome AF: 0.618

Gnomad4 AMR exome AF: 0.227

Gnomad4 ASJ exome AF: 0.273

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.0556

Gnomad4 FIN exome AF: 0.326

Gnomad4 NFE exome AF: 0.202

Gnomad4 OTH exome AF: 0.280

GnomAD4 genome AF: 0.343 AC: 52170 AN: 152078 Hom.: 10869 Cov.: 33 AF XY: 0.339 AC XY: 25193 AN XY: 74340

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.333

Alfa AF: 0.261 Hom.: 7505

Bravo AF: 0.360

Asia WGS AF: 0.144 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.5
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1054174; hg19: chr5-204952;