Genetic Variant C22orf46P:n.1993_1994dupGA (chr22-41695023-A-AAG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000472110.3(C22orf46P):n.1993_1994dupGA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 40081 hom., cov: 0)

Exomes 𝑓: 0.77 ( 4394 hom. )

Consequence

C22orf46P
ENST00000472110.3 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.892

Publications

5 publications found

Variant links:

Genes affected

C22orf46P (HGNC:):

C22orf46P links:

C22orf46P (HGNC:26294): (chromosome 22 open reading frame 46, pseudogene) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

C22orf46P links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000472110.3. 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
	C22orf46P	NR_160905.1		n.1907_1908dupGA		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
C22orf46P	ENST00000472110.3	TSL:3	n.1993_1994dupGA	non_coding_transcript_exon	Exon 3 of 3
C22orf46P	ENST00000654032.1		n.1781_1782dupGA	non_coding_transcript_exon	Exon 2 of 2
C22orf46P	ENST00000656592.1		n.1905_1906dupGA	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.716

AC:

108538

AN:

151558

Hom.:

40057

Cov.:

show subpopulations

Gnomad AFR

AF:

0.591

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.692

Gnomad EAS

AF:

0.916

Gnomad SAS

AF:

0.720

Gnomad FIN

AF:

0.762

Gnomad MID

AF:

0.713

Gnomad NFE

AF:

0.809

Gnomad OTH

AF:

0.711

GnomAD4 exome

AF:

0.766

AC:

11469

AN:

14966

Hom.:

4394

Cov.:

AF XY:

0.769

AC XY:

5453

AN XY:

7090

show subpopulations

African (AFR)

AF:

0.625

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.766

AC:

11261

AN:

14698

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.769

AC:

103

AN:

134

Other (OTH)

AF:

0.807

AC:

AN:

114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

140

281

421

562

702

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.716

AC:

108594

AN:

151678

Hom.:

40081

Cov.:

AF XY:

0.711

AC XY:

52624

AN XY:

74066

show subpopulations

African (AFR)

AF:

0.591

AC:

24439

AN:

41322

American (AMR)

AF:

0.547

AC:

8331

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.692

AC:

2396

AN:

3460

East Asian (EAS)

AF:

0.917

AC:

4719

AN:

5148

South Asian (SAS)

AF:

0.720

AC:

3459

AN:

4804

European-Finnish (FIN)

AF:

0.762

AC:

7973

AN:

10460

Middle Eastern (MID)

AF:

0.719

AC:

210

AN:

292

European-Non Finnish (NFE)

AF:

0.809

AC:

54940

AN:

67938

Other (OTH)

AF:

0.714

AC:

1508

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1435

2870

4306

5741

7176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.753

Hom.:

5359

Bravo

AF:

0.688

Asia WGS

AF:

0.809

AC:

2814

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.89

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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