Genetic Variant CARM1P1:n.2978377A>C (chr9-2978377-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.0755 in 152,240 control chromosomes in the GnomAD database, including 1,288 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 0.076 ( 1288 hom., cov: 33)

Consequence

CARM1P1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.855

Publications

1 publications found

Variant links:

Genes affected

CARM1P1 (HGNC:23392): (coactivator associated arginine methyltransferase 1 pseudogene 1)

CARM1P1 links:

ENSG00000290482 (HGNC:):

ENSG00000290482 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARM1P1		n.2978377A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARM1P1	ENST00000426329.6 link	n.427+14086T>G	intron_variant	Intron 4 of 10	6
ENSG00000290482	ENST00000497195.2 link	n.512+13657T>G	intron_variant	Intron 3 of 7	2
ENSG00000290482	ENST00000515723.2 link	n.994+13657T>G	intron_variant	Intron 7 of 11	5

Frequencies

GnomAD3 genomes

AF:

0.0754

AC:

11471

AN:

152122

Hom.:

1286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0349

Gnomad ASJ

AF:

0.00721

Gnomad EAS

AF:

0.00750

Gnomad SAS

AF:

0.00641

Gnomad FIN

AF:

0.00405

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00831

Gnomad OTH

AF:

0.0627

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0755

AC:

11498

AN:

152240

Hom.:

1288

Cov.:

AF XY:

0.0732

AC XY:

5449

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.244

AC:

10124

AN:

41504

American (AMR)

AF:

0.0348

AC:

533

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00721

AC:

AN:

3468

East Asian (EAS)

AF:

0.00732

AC:

AN:

5188

South Asian (SAS)

AF:

0.00663

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00405

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00829

AC:

564

AN:

68010

Other (OTH)

AF:

0.0620

AC:

131

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

458

917

1375

1834

2292

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0275

Hom.:

263

Bravo

AF:

0.0861

Asia WGS

AF:

0.0280

AC:

AN:

3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

7.5

(source)

DANN

Benign

0.88

PhyloP100

0.85

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over