dbSNP rs75847640: BRD10:p.Arg2081Gln (chr9-5919754-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001017969.3(BRD10):c.6242G>A(p.Arg2081Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000795 in 1,613,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00053 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00082 ( 0 hom. )

Consequence

BRD10
NM_001017969.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.394

Publications

5 publications found

Variant links:

Genes affected

BRD10 (HGNC:23378): (bromodomain containing 10)

BRD10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008494079).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017969.3. 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
	BRD10	NM_001017969.3	MANE Select	c.6242G>A	p.Arg2081Gln	missense	Exon 8 of 8	NP_001017969.2	Q5HYC2-1
	BRD10	NM_001438917.1		c.6152G>A	p.Arg2051Gln	missense	Exon 7 of 7	NP_001425846.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BRD10	ENST00000399933.8	TSL:5 MANE Select	c.6242G>A	p.Arg2081Gln	missense	Exon 8 of 8	ENSP00000382815.3	Q5HYC2-1
BRD10	ENST00000381461.6	TSL:5	c.6152G>A	p.Arg2051Gln	missense	Exon 7 of 7	ENSP00000370870.2	Q5HYC2-2
BRD10	ENST00000540714.1	TSL:5	n.*3829G>A		non_coding_transcript_exon	Exon 7 of 7	ENSP00000444949.1	H0YGV4

Frequencies

GnomAD3 genomes

AF:

0.000533

AC:

AN:

152046

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000655

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.000959

GnomAD2 exomes

AF:

0.000544

AC:

135

AN:

248066

AF XY:

0.000587

show subpopulations

Gnomad AFR exome

AF:

0.000194

Gnomad AMR exome

AF:

0.000117

Gnomad ASJ exome

AF:

0.0000996

Gnomad EAS exome

AF:

0.0000561

Gnomad FIN exome

AF:

0.0000465

Gnomad NFE exome

AF:

0.000970

Gnomad OTH exome

AF:

0.000331

GnomAD4 exome

AF:

0.000823

AC:

1202

AN:

1461210

Hom.:

Cov.:

AF XY:

0.000742

AC XY:

539

AN XY:

726838

show subpopulations

African (AFR)

AF:

0.000119

AC:

AN:

33478

American (AMR)

AF:

0.000135

AC:

AN:

44602

Ashkenazi Jewish (ASJ)

AF:

0.000115

AC:

AN:

26128

East Asian (EAS)

AF:

0.0000757

AC:

AN:

39622

South Asian (SAS)

AF:

0.000313

AC:

AN:

86198

European-Finnish (FIN)

AF:

0.000112

AC:

AN:

53388

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00100

AC:

1113

AN:

1111664

Other (OTH)

AF:

0.000663

AC:

AN:

60362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

147

221

294

368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

126

168

210

<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:

0.000532

AC:

AN:

152164

Hom.:

Cov.:

AF XY:

0.000538

AC XY:

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.000145

AC:

AN:

41508

American (AMR)

AF:

0.0000654

AC:

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.000415

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10580

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00103

AC:

AN:

68006

Other (OTH)

AF:

0.000949

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.00621

Hom.:

824

Bravo

AF:

0.000529

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00130

AC:

ESP6500AA

AF:

0.000266

AC:

ESP6500EA

AF:

0.000607

AC:

ExAC

AF:

0.000497

AC:

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.62

CADD

Benign

(source)

DANN

Benign

0.94

DEOGEN2

Benign

0.015

Eigen

Benign

-0.74

Eigen_PC

Benign

-0.59

FATHMM_MKL

Benign

0.53

LIST_S2

Benign

0.80

M_CAP

Benign

0.0031

MetaRNN

Benign

0.0085

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.1

PhyloP100

0.39

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.41

REVEL

Benign

0.018

Sift

Benign

0.45

Sift4G

Benign

0.12

Polyphen

0.0070

Vest4

0.11

MVP

0.10

ClinPred

0.0085

GERP RS

1.5

Varity_R

0.030

gMVP

0.063

Mutation Taster

=91/9

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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