dbSNP rs7538516: C1orf167:p.Arg776Gly (chr1-11776625-C-G) – 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_001010881.2(C1orf167):c.2326C>G(p.Arg776Gly) 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. 15/20 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: 35)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

C1orf167
NM_001010881.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0790

Publications

21 publications found

Variant links:

Genes affected

C1orf167 (HGNC:25262): (chromosome 1 open reading frame 167) Implicated in coronary artery disease. [provided by Alliance of Genome Resources, Apr 2022]

C1orf167 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=0.09313136).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf167	NM_001010881.2 link	c.2326C>G	p.Arg776Gly	missense_variant	Exon 10 of 21	ENST00000688073.1	NP_001010881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
C1orf167	ENST00000688073.1 link	c.2326C>G	p.Arg776Gly	missense_variant	Exon 10 of 21		NM_001010881.2	ENSP00000510540.1
C1orf167	ENST00000433342.6 link	c.1840C>G	p.Arg614Gly	missense_variant	Exon 10 of 21	5		ENSP00000414909.3
C1orf167	ENST00000312793.9 link	c.475C>G	p.Arg159Gly	missense_variant	Exon 3 of 14	2		ENSP00000317749.5
C1orf167	ENST00000484153.1 link	n.1371C>G		non_coding_transcript_exon_variant	Exon 8 of 9	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1042150

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

499988

African (AFR)

AF:

0.00

AC:

AN:

19472

American (AMR)

AF:

0.00

AC:

AN:

12070

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9392

East Asian (EAS)

AF:

0.00

AC:

AN:

8796

South Asian (SAS)

AF:

0.00

AC:

AN:

60304

European-Finnish (FIN)

AF:

0.00

AC:

AN:

23894

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3020

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

868516

Other (OTH)

AF:

0.00

AC:

AN:

36686

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

19603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.0032

Eigen

Benign

-0.96

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.084

LIST_S2

Benign

0.45

M_CAP

Benign

0.015

MetaRNN

Benign

0.093

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.90

PhyloP100

0.079

PROVEAN

Benign

-1.6

REVEL

Benign

0.18

Sift

Benign

0.15

Sift4G

Benign

0.25

Polyphen

0.88

Vest4

0.11

MutPred

0.29

Loss of helix (P = 0.0795);

MVP

0.099

MPC

0.43

ClinPred

0.44

GERP RS

0.71

Varity_R

0.092

gMVP

0.25

Mutation Taster

=99/1

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over