chr6-31150242-T-C

Variant names:

• chr6-31150242-T-C
• rs1265112
• NM_001105564.2:c.1213-27A>G

Variant summary

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

The NM_001105564.2(CCHCR1):​c.1213-27A>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 1,609,614 control chromosomes in the GnomAD database, including 76,978 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 (6197 hom., cov: 32)
  • Exomes 𝑓: 0.31 (70781 hom.)
• Consequence: CCHCR1 NM_001105564.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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=-0.74).
• 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 rank	MANE	Protein	UniProt
CCHCR1	NM_001105564.2	c.1213-27A>G		intron_variant	Intron 7 of 17	ENST00000396268.8	NP_001099034.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCHCR1	ENST00000396268.8	c.1213-27A>G		intron_variant	Intron 7 of 17	1	NM_001105564.2	ENSP00000379566.3

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42727 AN: 151960 Hom.: 6198 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.0831

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.306

GnomAD3 exomes AF: 0.278 AC: 69159 AN: 248440 Hom.: 10255 AF XY: 0.280 AC XY: 37619 AN XY: 134312

Gnomad AFR exome AF: 0.234

Gnomad AMR exome AF: 0.275

Gnomad ASJ exome AF: 0.439

Gnomad EAS exome AF: 0.0770

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: 446062 AN: 1457536 Hom.: 70781 Cov.: 33 AF XY: 0.304 AC XY: 220682 AN XY: 724988

Gnomad4 AFR exome AF: 0.228

Gnomad4 AMR exome AF: 0.276

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: 42744 AN: 152078 Hom.: 6197 Cov.: 32 AF XY: 0.278 AC XY: 20675 AN XY: 74344

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.0833

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.303

Alfa AF: 0.315 Hom.: 14440

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	-0.74
CADD	Benign	6.6
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs1265112; hg19: chr6-31118019; COSMIC: COSV66185490; COSMIC: COSV66185490;