10-87000265-C-G

Variant summary

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

The ENST00000444431.1(ENSG00000151303):​n.1152C>G 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 0.348 in 1,021,504 control chromosomes in the GnomAD database, including 66,073 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 0.43 ( 15655 hom., cov: 32)
Exomes 𝑓: 0.33 ( 50418 hom. )

Consequence

ENSG00000151303
ENST00000444431.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.117

Publications

1 publications found
Variant links:
Genes affected
BMS1P3 (HGNC:23651): (BMS1 pseudogene 3)
ADIRF (HGNC:24043): (adipogenesis regulatory factor) APM2 gene is exclusively expressed in adipose tissue. Its function is currently unknown. [provided by RefSeq, Jul 2008]
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]

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BMS1P3 n.87000265C>G intragenic_variant
AGAP11NR_171046.1 linkn.1306-54C>G intron_variant Intron 6 of 10

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000151303ENST00000444431.1 linkn.1152C>G non_coding_transcript_exon_variant Exon 4 of 7 1
BMS1P3ENST00000372011.4 linkn.816-54C>G intron_variant Intron 5 of 5 6
ENSG00000151303ENST00000433214.2 linkn.1002-54C>G intron_variant Intron 7 of 11 2

Frequencies

GnomAD3 genomes
AF:
0.431
AC:
65459
AN:
151826
Hom.:
15617
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.639
Gnomad AMI
AF:
0.255
Gnomad AMR
AF:
0.492
Gnomad ASJ
AF:
0.403
Gnomad EAS
AF:
0.244
Gnomad SAS
AF:
0.353
Gnomad FIN
AF:
0.312
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.335
Gnomad OTH
AF:
0.403
GnomAD4 exome
AF:
0.333
AC:
289761
AN:
869560
Hom.:
50418
Cov.:
11
AF XY:
0.335
AC XY:
143952
AN XY:
430108
show subpopulations
African (AFR)
AF:
0.646
AC:
10828
AN:
16754
American (AMR)
AF:
0.554
AC:
8641
AN:
15590
Ashkenazi Jewish (ASJ)
AF:
0.398
AC:
3882
AN:
9756
East Asian (EAS)
AF:
0.235
AC:
3722
AN:
15826
South Asian (SAS)
AF:
0.352
AC:
16359
AN:
46476
European-Finnish (FIN)
AF:
0.310
AC:
5387
AN:
17356
Middle Eastern (MID)
AF:
0.410
AC:
811
AN:
1976
European-Non Finnish (NFE)
AF:
0.321
AC:
228937
AN:
713366
Other (OTH)
AF:
0.345
AC:
11194
AN:
32460
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
8599
17198
25796
34395
42994
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
8508
17016
25524
34032
42540
<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:
0.431
AC:
65543
AN:
151944
Hom.:
15655
Cov.:
32
AF XY:
0.428
AC XY:
31824
AN XY:
74270
show subpopulations
African (AFR)
AF:
0.639
AC:
26460
AN:
41430
American (AMR)
AF:
0.492
AC:
7513
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.403
AC:
1396
AN:
3466
East Asian (EAS)
AF:
0.244
AC:
1261
AN:
5162
South Asian (SAS)
AF:
0.353
AC:
1698
AN:
4816
European-Finnish (FIN)
AF:
0.312
AC:
3285
AN:
10524
Middle Eastern (MID)
AF:
0.378
AC:
111
AN:
294
European-Non Finnish (NFE)
AF:
0.335
AC:
22739
AN:
67968
Other (OTH)
AF:
0.401
AC:
847
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1736
3471
5207
6942
8678
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
582
1164
1746
2328
2910
<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:
0.216
Hom.:
436
Bravo
AF:
0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
5.1
DANN
Benign
0.20
PhyloP100
-0.12

Splicing

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

Publications

Other links and lift over

dbSNP: rs1240373; hg19: chr10-88760022; COSMIC: COSV64393547; API