dbSNP rs3088232: BRDT:p.Asn410Lys (chr1-91979700-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_207189.4(BRDT):c.1230C>G(p.Asn410Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,612,400 control chromosomes in the GnomAD database, including 46,807 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.18 ( 3133 hom., cov: 32)

Exomes 𝑓: 0.24 ( 43674 hom. )

Consequence

BRDT
NM_207189.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219

Variant links:

Genes affected

BRDT (HGNC:1105): (bromodomain testis associated) BRDT is similar to the RING3 protein family. It possesses 2 bromodomain motifs and a PEST sequence (a cluster of proline, glutamic acid, serine, and threonine residues), characteristic of proteins that undergo rapid intracellular degradation. The bromodomain is found in proteins that regulate transcription. Several transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

BRDT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0022077262).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRDT	NM_207189.4 link	c.1230C>G	p.Asn410Lys	missense_variant	Exon 8 of 19	ENST00000399546.7	NP_997072.2	Q58F21-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRDT	ENST00000399546.7 link	c.1230C>G	p.Asn410Lys	missense_variant	Exon 8 of 19	2	NM_207189.4	ENSP00000387822.3		Q58F21-1

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27430

AN:

152018

Hom.:

3122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0540

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.0320

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.188

GnomAD3 exomes

AF:

0.212

AC:

52982

AN:

250326

Hom.:

6402

AF XY:

0.216

AC XY:

29189

AN XY:

135340

show subpopulations

Gnomad AFR exome

AF:

0.0472

Gnomad AMR exome

AF:

0.224

Gnomad ASJ exome

AF:

0.253

Gnomad EAS exome

AF:

0.0220

Gnomad SAS exome

AF:

0.213

Gnomad FIN exome

AF:

0.255

Gnomad NFE exome

AF:

0.250

Gnomad OTH exome

AF:

0.215

GnomAD4 exome

AF:

0.238

AC:

347928

AN:

1460264

Hom.:

43674

Cov.:

AF XY:

0.238

AC XY:

173238

AN XY:

726406

show subpopulations

Gnomad4 AFR exome

AF:

0.0463

Gnomad4 AMR exome

AF:

0.220

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.0434

Gnomad4 SAS exome

AF:

0.215

Gnomad4 FIN exome

AF:

0.251

Gnomad4 NFE exome

AF:

0.254

Gnomad4 OTH exome

AF:

0.223

GnomAD4 genome

AF:

0.181

AC:

27462

AN:

152136

Hom.:

3133

Cov.:

AF XY:

0.179

AC XY:

13344

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.0539

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.0319

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.247

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.186

Alfa

AF:

0.217

Hom.:

2479

Bravo

AF:

0.170

TwinsUK

AF:

0.261

AC:

968

ALSPAC

AF:

0.257

AC:

989

ESP6500AA

AF:

0.0590

AC:

260

ESP6500EA

AF:

0.248

AC:

2137

ExAC

AF:

0.211

AC:

25631

Asia WGS

AF:

0.115

AC:

399

AN:

3478

EpiCase

AF:

0.244

EpiControl

AF:

0.246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.71

CADD

Benign

4.4

DANN

Uncertain

0.98

DEOGEN2

Benign

0.063

T;.;.;.;T;T

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.53

FATHMM_MKL

Benign

0.26

LIST_S2

Benign

0.10

.;T;T;T;T;T

MetaRNN

Benign

0.0022

T;T;T;T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.1

L;.;.;.;.;L

PrimateAI

Benign

0.26

PROVEAN

Benign

-1.4

N;N;N;.;N;N

REVEL

Benign

0.040

Sift

Benign

0.28

T;T;T;.;T;T

Sift4G

Benign

0.55

T;T;T;T;T;T

Polyphen

0.0030

B;.;.;.;.;B

Vest4

0.056

MutPred

0.27

Gain of ubiquitination at N410 (P = 0.0054);.;.;.;Gain of ubiquitination at N410 (P = 0.0054);Gain of ubiquitination at N410 (P = 0.0054);

MPC

0.091

ClinPred

0.0037

GERP RS

3.8

Varity_R

0.12

gMVP

0.070

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over