Variant 5-204962-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.714

Variant links:

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]

CCDC127 links:

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ACMG classification

Classification made for transcript

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 linkuse as main transcript	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 linkuse as main transcript	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.:

show subpopulations

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.:

AF XY:

0.121

AC XY:

2435

AN XY:

20094

show subpopulations

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.:

AF XY:

0.203

AC XY:

15079

AN XY:

74402

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over