Genetic Variant ENST00000376620.3:n.903T>C (chr1-11778042-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000376620.3(C1orf167-AS1):n.903T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,854 control chromosomes in the GnomAD database, including 35,629 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 ( 35599 hom., cov: 29)

Exomes 𝑓: 0.73 ( 30 hom. )

Consequence

C1orf167-AS1
ENST00000376620.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0870

Publications

7 publications found

Variant links:

Genes affected

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

C1orf167-AS1 links:

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: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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: ENST00000376620.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf167	NM_001010881.2	MANE Select	c.2340-618A>G		intron	N/A	NP_001010881.1
	C1orf167-AS1	NR_126000.1		n.903T>C		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
C1orf167-AS1	ENST00000376620.3	TSL:1	n.903T>C	non_coding_transcript_exon	Exon 3 of 3
C1orf167	ENST00000688073.1	MANE Select	c.2340-618A>G	intron	N/A	ENSP00000510540.1
C1orf167	ENST00000484153.1	TSL:2	n.2298A>G	non_coding_transcript_exon	Exon 9 of 9

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

102685

AN:

151636

Hom.:

35586

Cov.:

show subpopulations

Gnomad AFR

AF:

0.531

Gnomad AMI

AF:

0.670

Gnomad AMR

AF:

0.777

Gnomad ASJ

AF:

0.657

Gnomad EAS

AF:

0.887

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.784

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.714

Gnomad OTH

AF:

0.665

GnomAD4 exome

AF:

0.730

AC:

AN:

100

Hom.:

Cov.:

AF XY:

0.743

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.795

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.563

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.677

AC:

102744

AN:

151754

Hom.:

35599

Cov.:

AF XY:

0.681

AC XY:

50520

AN XY:

74146

show subpopulations

African (AFR)

AF:

0.531

AC:

21960

AN:

41360

American (AMR)

AF:

0.777

AC:

11829

AN:

15220

Ashkenazi Jewish (ASJ)

AF:

0.657

AC:

2280

AN:

3470

East Asian (EAS)

AF:

0.887

AC:

4565

AN:

5146

South Asian (SAS)

AF:

0.662

AC:

3193

AN:

4820

European-Finnish (FIN)

AF:

0.784

AC:

8253

AN:

10530

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.714

AC:

48493

AN:

67902

Other (OTH)

AF:

0.663

AC:

1395

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1605

3211

4816

6422

8027

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<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:

0.676

Hom.:

4935

Bravo

AF:

0.670

Asia WGS

AF:

0.742

AC:

2582

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.5

(source)

DANN

Benign

0.83

PhyloP100

-0.087

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over