Genetic Variant TRABD:n.2302G>C (chr22-50199493-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000463233.1(TRABD):n.2302G>C 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 0.0979 in 202,468 control chromosomes in the GnomAD database, including 1,217 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 0.097 ( 900 hom., cov: 34)

Exomes 𝑓: 0.10 ( 317 hom. )

Consequence

TRABD
ENST00000463233.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.38

Publications

15 publications found

Variant links:

Genes affected

TRABD (HGNC:28805): (TraB domain containing)

TRABD links:

TRABD-AS1 (HGNC:56049): (TRABD antisense RNA 1)

TRABD-AS1 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRABD	NM_001320485.2 link	c.*974G>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000380909.9	NP_001307414.1	Q9H4I3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRABD	ENST00000380909.9 link	c.*974G>C		3_prime_UTR_variant	Exon 10 of 10	5	NM_001320485.2	ENSP00000370295.4		Q9H4I3-1

Frequencies

GnomAD3 genomes

AF:

0.0969

AC:

14753

AN:

152202

Hom.:

901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0238

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0962

Gnomad ASJ

AF:

0.0821

Gnomad EAS

AF:

0.0311

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.0965

GnomAD4 exome

AF:

0.101

AC:

5077

AN:

50148

Hom.:

317

Cov.:

AF XY:

0.102

AC XY:

2578

AN XY:

25184

show subpopulations

African (AFR)

AF:

0.0200

AC:

AN:

1996

American (AMR)

AF:

0.0687

AC:

AN:

1382

Ashkenazi Jewish (ASJ)

AF:

0.0690

AC:

150

AN:

2174

East Asian (EAS)

AF:

0.0201

AC:

AN:

3334

South Asian (SAS)

AF:

0.200

AC:

303

AN:

1518

European-Finnish (FIN)

AF:

0.0978

AC:

220

AN:

2250

Middle Eastern (MID)

AF:

0.111

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.114

AC:

3805

AN:

33492

Other (OTH)

AF:

0.0983

AC:

365

AN:

3714

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

218

436

655

873

1091

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0968

AC:

14749

AN:

152320

Hom.:

900

Cov.:

AF XY:

0.0991

AC XY:

7378

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.0237

AC:

987

AN:

41574

American (AMR)

AF:

0.0960

AC:

1470

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0821

AC:

285

AN:

3472

East Asian (EAS)

AF:

0.0310

AC:

161

AN:

5190

South Asian (SAS)

AF:

0.214

AC:

1034

AN:

4828

European-Finnish (FIN)

AF:

0.125

AC:

1330

AN:

10616

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.134

AC:

9114

AN:

68012

Other (OTH)

AF:

0.0969

AC:

205

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

705

1410

2116

2821

3526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0637

Hom.:

Bravo

AF:

0.0890

Asia WGS

AF:

0.112

AC:

390

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.73

(source)

DANN

Benign

0.47

PhyloP100

-3.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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