6-31144825-G-C

Variant summary

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

The NM_001105564.2(CCHCR1):c.2066-37C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 1,607,840 control chromosomes in the GnomAD database, including 76,992 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 0.28 (6184 hom., cov: 30)
  • Exomes 𝑓: 0.31 (70808 hom.)
• Consequence: CCHCR1 NM_001105564.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCHCR1	NM_001105564.2	c.2066-37C>G		intron_variant		ENST00000396268.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCHCR1	ENST00000396268.8	c.2066-37C>G		intron_variant		1	NM_001105564.2	A2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42642 AN: 151758 Hom.: 6185 Cov.: 30

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.306

GnomAD3 exomes AF: 0.279 AC: 69989 AN: 251150 Hom.: 10513 AF XY: 0.280 AC XY: 38074 AN XY: 135750

Gnomad AFR exome AF: 0.234

Gnomad AMR exome AF: 0.275

Gnomad ASJ exome AF: 0.439

Gnomad EAS exome AF: 0.0771

Gnomad SAS exome AF: 0.235

Gnomad FIN exome AF: 0.302

Gnomad NFE exome AF: 0.311

Gnomad OTH exome AF: 0.294

GnomAD4 exome AF: 0.306 AC: 446073 AN: 1455964 Hom.: 70808 Cov.: 30 AF XY: 0.305 AC XY: 220758 AN XY: 724412

Gnomad4 AFR exome AF: 0.228

Gnomad4 AMR exome AF: 0.277

Gnomad4 ASJ exome AF: 0.440

Gnomad4 EAS exome AF: 0.0681

Gnomad4 SAS exome AF: 0.237

Gnomad4 FIN exome AF: 0.302

Gnomad4 NFE exome AF: 0.320

Gnomad4 OTH exome AF: 0.314

GnomAD4 genome AF: 0.281 AC: 42659 AN: 151876 Hom.: 6184 Cov.: 30 AF XY: 0.278 AC XY: 20619 AN XY: 74194

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.0838

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.303

Alfa AF: 0.316 Hom.: 1596

Bravo AF: 0.279

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.9
Dann	Benign	0.60

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: rs1265078; hg19: chr6-31112602; COSMIC: COSV52550411; COSMIC: COSV52550411;