Genetic Variant ENSG00000151303:n.44G>A (chr10-86992449-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000444431.1(ENSG00000151303):n.44G>A 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 0.372 in 236,584 control chromosomes in the GnomAD database, including 17,830 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 0.39 ( 12730 hom., cov: 32)

Exomes 𝑓: 0.33 ( 5100 hom. )

Consequence

ENSG00000151303
ENST00000444431.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.38

Publications

5 publications found

Variant links:

Genes affected

ENSG00000151303 (HGNC:):

ENSG00000151303 links:

BMS1P3 (HGNC:23651): (BMS1 pseudogene 3)

BMS1P3 links:

ADIRF (HGNC:24043): (adipogenesis regulatory factor) APM2 gene is exclusively expressed in adipose tissue. Its function is currently unknown. [provided by RefSeq, Jul 2008]

ADIRF links:

AGAP11 (HGNC:29421): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 11) Predicted to enable GTPase activator activity and metal ion binding activity. Predicted to be involved in regulation of catalytic activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

AGAP11 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=-0.6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGAP11	NR_171046.1 link	n.871G>A		non_coding_transcript_exon_variant	Exon 3 of 11
BMS1P3		n.86992449G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000151303	ENST00000444431.1 link	n.44G>A	non_coding_transcript_exon_variant	Exon 1 of 7	1
BMS1P3	ENST00000372011.4 link	n.197G>A	non_coding_transcript_exon_variant	Exon 1 of 6	6
ENSG00000151303	ENST00000433214.2 link	n.567G>A	non_coding_transcript_exon_variant	Exon 4 of 12	2

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

59966

AN:

151972

Hom.:

12701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.535

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.475

Gnomad ASJ

AF:

0.390

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.374

GnomAD4 exome

AF:

0.331

AC:

27935

AN:

84494

Hom.:

5100

Cov.:

AF XY:

0.327

AC XY:

15733

AN XY:

48106

show subpopulations

African (AFR)

AF:

0.535

AC:

1094

AN:

2046

American (AMR)

AF:

0.558

AC:

4996

AN:

8946

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

422

AN:

1180

East Asian (EAS)

AF:

0.218

AC:

1139

AN:

5216

South Asian (SAS)

AF:

0.329

AC:

2577

AN:

7828

European-Finnish (FIN)

AF:

0.278

AC:

4499

AN:

16168

Middle Eastern (MID)

AF:

0.391

AC:

647

AN:

1654

European-Non Finnish (NFE)

AF:

0.302

AC:

11559

AN:

38244

Other (OTH)

AF:

0.312

AC:

1002

AN:

3212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.443

Heterozygous variant carriers

708

1416

2125

2833

3541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.395

AC:

60035

AN:

152090

Hom.:

12730

Cov.:

AF XY:

0.394

AC XY:

29274

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.535

AC:

22174

AN:

41460

American (AMR)

AF:

0.475

AC:

7261

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.390

AC:

1352

AN:

3466

East Asian (EAS)

AF:

0.237

AC:

1228

AN:

5184

South Asian (SAS)

AF:

0.346

AC:

1670

AN:

4820

European-Finnish (FIN)

AF:

0.305

AC:

3233

AN:

10588

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.324

AC:

22000

AN:

67976

Other (OTH)

AF:

0.373

AC:

784

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1794

3587

5381

7174

8968

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.387

Hom.:

1745

Bravo

AF:

0.412

Asia WGS

AF:

0.289

AC:

1004

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

4.3

(source)

DANN

Benign

0.33

PhyloP100

3.4

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over