Genetic Variant C1orf141:p.Met340CysfsTer7 (chr1-67093186-CTCATT-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_001276351.2(C1orf141):c.1017_1021delAATGA(p.Met340CysfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00911 in 1,613,812 control chromosomes in the GnomAD database, including 79 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0069 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0093 ( 71 hom. )

Consequence

C1orf141
NM_001276351.2 frameshift

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.13

Publications

4 publications found

Variant links:

Genes affected

C1orf141 (HGNC:32044): (chromosome 1 open reading frame 141)

C1orf141 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP6

Variant 1-67093186-CTCATT-C is Benign according to our data. Variant chr1-67093186-CTCATT-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 778232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001276351.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
C1orf141	NM_001276351.2	MANE Select	c.1017_1021delAATGA	p.Met340CysfsTer7	frameshift	Exon 8 of 8	NP_001263280.1	Q5JVX7-1
C1orf141	NM_001276352.2		c.389_393delAATGA		3_prime_UTR	Exon 9 of 9	NP_001263281.1	F2Z2X7
C1orf141	NR_075077.2		n.1330_1334delAATGA		non_coding_transcript_exon	Exon 10 of 10

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
C1orf141	ENST00000684719.1	MANE Select	c.1017_1021delAATGA	p.Met340CysfsTer7	frameshift	Exon 8 of 8	ENSP00000507487.1	Q5JVX7-1
C1orf141	ENST00000544837.5	TSL:1	n.829_833delAATGA		non_coding_transcript_exon	Exon 10 of 10	ENSP00000444018.2	A0A0A0MTM1
C1orf141	ENST00000544837.5	TSL:1	n.829_833delAATGA		3_prime_UTR	Exon 10 of 10	ENSP00000444018.2	A0A0A0MTM1

Frequencies

GnomAD3 genomes

AF:

0.00686

AC:

1044

AN:

152086

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00196

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00845

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.00368

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.00862

GnomAD2 exomes

AF:

0.00603

AC:

1516

AN:

251282

AF XY:

0.00581

show subpopulations

Gnomad AFR exome

AF:

0.00172

Gnomad AMR exome

AF:

0.00335

Gnomad ASJ exome

AF:

0.0229

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00416

Gnomad NFE exome

AF:

0.00871

Gnomad OTH exome

AF:

0.00767

GnomAD4 exome

AF:

0.00934

AC:

13656

AN:

1461608

Hom.:

AF XY:

0.00900

AC XY:

6544

AN XY:

727118

show subpopulations

African (AFR)

AF:

0.00158

AC:

AN:

33462

American (AMR)

AF:

0.00364

AC:

163

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0221

AC:

577

AN:

26126

East Asian (EAS)

AF:

0.00

AC:

AN:

39664

South Asian (SAS)

AF:

0.000661

AC:

AN:

86246

European-Finnish (FIN)

AF:

0.00502

AC:

268

AN:

53418

Middle Eastern (MID)

AF:

0.00226

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.0108

AC:

12019

AN:

1111826

Other (OTH)

AF:

0.00838

AC:

506

AN:

60380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

703

1405

2108

2810

3513

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.00686

AC:

1044

AN:

152204

Hom.:

Cov.:

AF XY:

0.00638

AC XY:

475

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.00195

AC:

AN:

41534

American (AMR)

AF:

0.00843

AC:

129

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0228

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5182

South Asian (SAS)

AF:

0.000828

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00368

AC:

AN:

10598

Middle Eastern (MID)

AF:

0.00685

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0102

AC:

691

AN:

67986

Other (OTH)

AF:

0.00853

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

140

186

233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00785

Hom.:

Bravo

AF:

0.00678

Asia WGS

AF:

0.000289

AC:

AN:

3474

EpiCase

AF:

0.0105

EpiControl

AF:

0.0103

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.1

Mutation Taster

=188/12

polymorphism

(source)

Splicing

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