dbSNP rs13173911: CCDC127:c.121+2431G>A (chr5-214298-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_145265.3(CCDC127):c.121+2431G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,998 control chromosomes in the GnomAD database, including 13,081 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 0.39 ( 13077 hom., cov: 31)

Exomes 𝑓: 0.60 ( 4 hom. )

Consequence

CCDC127
NM_145265.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.88

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:

ENSG00000260774 (HGNC:):

ENSG00000260774 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC127	NM_145265.3 link	c.121+2431G>A		intron_variant	Intron 2 of 2	ENST00000296824.4	NP_660308.1	Q96BQ5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC127	ENST00000296824.4 link	c.121+2431G>A	intron_variant	Intron 2 of 2	1	NM_145265.3	ENSP00000296824.2	Q96BQ5
CCDC127	ENST00000441693.2 link	c.121+2431G>A	intron_variant	Intron 1 of 1	2		ENSP00000411206.2	D6R9R2
ENSG00000260774	ENST00000565521.1 link	n.2481G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58650

AN:

151860

Hom.:

13081

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.381

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.450

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.512

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.393

GnomAD4 exome

AF:

0.600

AC:

AN:

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.563

GnomAD4 genome

AF:

0.386

AC:

58653

AN:

151978

Hom.:

13077

Cov.:

AF XY:

0.387

AC XY:

28765

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.381

Gnomad4 ASJ

AF:

0.450

Gnomad4 EAS

AF:

0.281

Gnomad4 SAS

AF:

0.512

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.395

Alfa

AF:

0.432

Hom.:

1901

Bravo

AF:

0.362

Asia WGS

AF:

0.374

AC:

1298

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.020

DANN

Benign

0.47

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