rs11967883

Positions:

• chr6-31144577-C-T

Variant summary

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

The NM_001105564.2(CCHCR1):​c.2167+110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 713,482 control chromosomes in the GnomAD database, including 1,587 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 0.064 (514 hom., cov: 31)
  • Exomes 𝑓: 0.042 (1073 hom.)
• Consequence: CCHCR1 NM_001105564.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

CCHCR1 (HGNC:13930): (coiled-coil alpha-helical rod protein 1) This gene encodes a protein with five coiled-coil alpha-helical rod domains that is thought to act as a regulator of mRNA metabolism through its interaction with mRNA-decapping protein 4. It localizes to P-bodies, the site of mRNA metabolism, with an N-terminus that is required for this subcellular localization, suggesting it is a P-body component. Naturally occurring mutations in this gene are associated with psoriasis. [provided by RefSeq, May 2017]

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 (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCHCR1	NM_001105564.2	c.2167+110G>A		intron_variant		ENST00000396268.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCHCR1	ENST00000396268.8	c.2167+110G>A		intron_variant		1	NM_001105564.2	A2

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9703 AN: 152008 Hom.: 512 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0636

GnomAD4 exome AF: 0.0425 AC: 23849 AN: 561356 Hom.: 1073 Cov.: 7 AF XY: 0.0408 AC XY: 12103 AN XY: 296318

Gnomad4 AFR exome AF: 0.140

Gnomad4 AMR exome AF: 0.0263

Gnomad4 ASJ exome AF: 0.0273

Gnomad4 EAS exome AF: 0.186

Gnomad4 SAS exome AF: 0.0360

Gnomad4 FIN exome AF: 0.0593

Gnomad4 NFE exome AF: 0.0243

Gnomad4 OTH exome AF: 0.0482

GnomAD4 genome AF: 0.0638 AC: 9707 AN: 152126 Hom.: 514 Cov.: 31 AF XY: 0.0650 AC XY: 4832 AN XY: 74370

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0338

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0241

Gnomad4 OTH AF: 0.0644

Alfa AF: 0.0309 Hom.: 84

Bravo AF: 0.0671

Asia WGS AF: 0.114 AC: 394 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	6.7
DANN	Benign	0.66

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: rs11967883; hg19: chr6-31112354;