dbSNP rs1576: CCHCR1:p.Ser865Phe (chr6-31142614-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001105564.2(CCHCR1):c.2594C>T(p.Ser865Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

CCHCR1
NM_001105564.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473

Publications

62 publications found

Variant links:

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]

CCHCR1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.06960225).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105564.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CCHCR1	NM_001105564.2	MANE Select	c.2594C>T	p.Ser865Phe	missense	Exon 18 of 18	NP_001099034.1	Q8TD31-2
CCHCR1	NM_001394641.1		c.2621C>T	p.Ser874Phe	missense	Exon 18 of 18	NP_001381570.1
CCHCR1	NM_001105563.3		c.2486C>T	p.Ser829Phe	missense	Exon 18 of 18	NP_001099033.1	Q8TD31-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CCHCR1	ENST00000396268.8	TSL:1 MANE Select	c.2594C>T	p.Ser865Phe	missense	Exon 18 of 18	ENSP00000379566.3	Q8TD31-2
CCHCR1	ENST00000451521.6	TSL:1	c.2486C>T	p.Ser829Phe	missense	Exon 18 of 18	ENSP00000401039.2	Q8TD31-3
CCHCR1	ENST00000376266.9	TSL:1	c.2327C>T	p.Ser776Phe	missense	Exon 18 of 18	ENSP00000365442.5	Q8TD31-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000399

AC:

AN:

250546

AF XY:

0.00000738

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000881

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

AC:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.75

CADD

Benign

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.0052

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.82

M_CAP

Benign

0.0074

MetaRNN

Benign

0.070

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.4

PhyloP100

-0.47

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.60

REVEL

Benign

0.038

Sift

Uncertain

0.0070

Sift4G

Uncertain

0.018

Polyphen

0.0

Vest4

0.10

MutPred

0.19

Loss of phosphorylation at S776 (P = 0.0571)

MVP

0.13

MPC

0.68

ClinPred

0.082

GERP RS

-5.4

Varity_R

0.060

gMVP

0.14

Mutation Taster

=99/1

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over