rs13173911

chr5-214298-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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88

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]

(HGNC:):

ACMG classification

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/exons	MANE	UniProt
CCDC127	NM_145265.3	c.121+2431G>A		intron_variant		ENST00000296824.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC127	ENST00000296824.4	c.121+2431G>A		intron_variant		1	NM_145265.3	P1
	ENST00000565521.1	n.2481G>A		non_coding_transcript_exon_variant	2/2	2
CCDC127	ENST00000441693.2	c.121+2431G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58650 AN: 151860 Hom.: 13081 Cov.: 31

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: 12 AN: 20 Hom.: 4 Cov.: 0 AF XY: 0.667 AC XY: 8 AN XY: 12

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.563

GnomAD4 genome AF: 0.386 AC: 58653 AN: 151978 Hom.: 13077 Cov.: 31 AF XY: 0.387 AC XY: 28765 AN XY: 74276

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

Other links and lift over

dbSNP: rs13173911; hg19: chr5-214413;