rs13474

Positions:

• chr5-204962-G-C
• chr5-204962-G-T

Variant summary

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

The NM_145265.3(CCDC127):​c.*335C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 192,050 control chromosomes in the GnomAD database, including 4,946 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 0.20 (4503 hom., cov: 33)
  • Exomes 𝑓: 0.12 (443 hom.)
• Consequence: CCDC127 NM_145265.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC127	NM_145265.3	c.*335C>G		3_prime_UTR_variant	3/3	ENST00000296824.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC127	ENST00000296824.4	c.*335C>G		3_prime_UTR_variant	3/3	1	NM_145265.3	P1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31072 AN: 152032 Hom.: 4492 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.000960

Gnomad SAS AF: 0.0755

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.122 AC: 4874 AN: 39900 Hom.: 443 Cov.: 0 AF XY: 0.121 AC XY: 2435 AN XY: 20094

Gnomad4 AFR exome AF: 0.392

Gnomad4 AMR exome AF: 0.148

Gnomad4 ASJ exome AF: 0.101

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0462

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.205 AC: 31117 AN: 152150 Hom.: 4503 Cov.: 33 AF XY: 0.203 AC XY: 15079 AN XY: 74402

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.000962

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.183

Alfa AF: 0.0870 Hom.: 152

Bravo AF: 0.210

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.57

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: rs13474; hg19: chr5-205077;