rs3094662

Positions:

• chr6-31154168-A-C
• chr6-31154168-A-G

Variant summary

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

The NM_001105564.2(CCHCR1):​c.801+328T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,812 control chromosomes in the GnomAD database, including 2,420 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 0.17 (2420 hom., cov: 32)
• Consequence: CCHCR1 NM_001105564.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCHCR1	NM_001105564.2	c.801+328T>G		intron_variant		ENST00000396268.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCHCR1	ENST00000396268.8	c.801+328T>G		intron_variant		1	NM_001105564.2	A2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25930 AN: 151694 Hom.: 2416 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.156

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.171 AC: 25939 AN: 151812 Hom.: 2420 Cov.: 32 AF XY: 0.165 AC XY: 12266 AN XY: 74226

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0404

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.153

Alfa AF: 0.169 Hom.: 760

Bravo AF: 0.168

Asia WGS AF: 0.0750 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.9
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3094662; hg19: chr6-31121945;