Genetic Variant C1orf167:c.2339+353C>G (chr1-11776991-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001010881.2(C1orf167):c.2339+353C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 154,792 control chromosomes in the GnomAD database, including 36,322 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 0.68 ( 35439 hom., cov: 34)

Exomes 𝑓: 0.75 ( 883 hom. )

Consequence

C1orf167
NM_001010881.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.263

Publications

7 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:

C1orf167-AS1 (HGNC:41091): (C1orf167 antisense RNA 1)

C1orf167-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010881.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf167	NM_001010881.2	MANE Select	c.2339+353C>G		intron	N/A	NP_001010881.1	Q5SNV9-1
	C1orf167-AS1	NR_126000.1		n.*86G>C		downstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C1orf167	ENST00000688073.1	MANE Select	c.2339+353C>G	intron	N/A	ENSP00000510540.1	Q5SNV9-1
C1orf167	ENST00000433342.6	TSL:5	c.1853+353C>G	intron	N/A	ENSP00000414909.3	A0AAG2QDU5
C1orf167	ENST00000312793.9	TSL:2	c.488+353C>G	intron	N/A	ENSP00000317749.5	H7BXQ2

Frequencies

GnomAD3 genomes

AF:

0.676

AC:

102472

AN:

151586

Hom.:

35427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.669

Gnomad AMR

AF:

0.776

Gnomad ASJ

AF:

0.657

Gnomad EAS

AF:

0.887

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.781

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.714

Gnomad OTH

AF:

0.667

GnomAD4 exome

AF:

0.751

AC:

2321

AN:

3090

Hom.:

883

AF XY:

0.752

AC XY:

1226

AN XY:

1630

show subpopulations

African (AFR)

AF:

0.600

AC:

AN:

American (AMR)

AF:

0.847

AC:

586

AN:

692

Ashkenazi Jewish (ASJ)

AF:

0.579

AC:

AN:

East Asian (EAS)

AF:

0.900

AC:

AN:

South Asian (SAS)

AF:

0.660

AC:

215

AN:

326

European-Finnish (FIN)

AF:

0.712

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.735

AC:

1320

AN:

1796

Other (OTH)

AF:

0.765

AC:

104

AN:

136

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

110

138

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.676

AC:

102531

AN:

151702

Hom.:

35439

Cov.:

AF XY:

0.680

AC XY:

50410

AN XY:

74120

show subpopulations

African (AFR)

AF:

0.529

AC:

21863

AN:

41362

American (AMR)

AF:

0.776

AC:

11856

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.657

AC:

2279

AN:

3470

East Asian (EAS)

AF:

0.887

AC:

4575

AN:

5158

South Asian (SAS)

AF:

0.663

AC:

3185

AN:

4804

European-Finnish (FIN)

AF:

0.781

AC:

8209

AN:

10512

Middle Eastern (MID)

AF:

0.572

AC:

166

AN:

290

European-Non Finnish (NFE)

AF:

0.714

AC:

48392

AN:

67820

Other (OTH)

AF:

0.665

AC:

1400

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1724

3448

5171

6895

8619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

800

1600

2400

3200

4000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.617

Hom.:

2070

Bravo

AF:

0.670

Asia WGS

AF:

0.741

AC:

2578

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.9

(source)

DANN

Benign

0.16

PhyloP100

-0.26

Mutation Taster

=100/0

polymorphism (auto)

(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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over