6-31154349-G-C

Position:

• chr6-31154349-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.801+147C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 679,004 control chromosomes in the GnomAD database, including 124,242 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 0.60 (27563 hom., cov: 32)
  • Exomes 𝑓: 0.60 (96679 hom.)
• Consequence: CCHCR1 NM_001105564.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCHCR1	NM_001105564.2	c.801+147C>G		intron_variant		ENST00000396268.8	NP_001099034.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCHCR1	ENST00000396268.8	c.801+147C>G		intron_variant		1	NM_001105564.2	ENSP00000379566	A2

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91401 AN: 151960 Hom.: 27563 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.623

GnomAD4 exome AF: 0.603 AC: 317554 AN: 526928 Hom.: 96679 AF XY: 0.603 AC XY: 167408 AN XY: 277468

Gnomad4 AFR exome AF: 0.580

Gnomad4 AMR exome AF: 0.659

Gnomad4 ASJ exome AF: 0.761

Gnomad4 EAS exome AF: 0.601

Gnomad4 SAS exome AF: 0.632

Gnomad4 FIN exome AF: 0.626

Gnomad4 NFE exome AF: 0.584

Gnomad4 OTH exome AF: 0.614

GnomAD4 genome AF: 0.601 AC: 91436 AN: 152076 Hom.: 27563 Cov.: 32 AF XY: 0.605 AC XY: 44999 AN XY: 74348

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.624

Alfa AF: 0.603 Hom.: 15267

Bravo AF: 0.606

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.55

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: rs2073717; hg19: chr6-31122126;