Genetic Variant ENST00000572588.1:n.3032C>T (chr16-14261908-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000572588.1(MRTFB):n.3032C>T 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 0.176 in 153,408 control chromosomes in the GnomAD database, including 4,612 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 0.18 ( 4604 hom., cov: 33)

Exomes 𝑓: 0.048 ( 8 hom. )

Consequence

MRTFB
ENST00000572588.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.07

Publications

8 publications found

Variant links:

Genes affected

MRTFB (HGNC:29819): (myocardin related transcription factor B) Enables transcription coactivator activity. Involved in positive regulation of pri-miRNA transcription by RNA polymerase II and positive regulation of striated muscle tissue development. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MRTFB Gene-Disease associations (from GenCC):

neurodevelopmental disorder
Inheritance: AD Classification: LIMITED Submitted by: G2P

MRTFB links:

ENSG00000305939 (HGNC:):

ENSG00000305939 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRTFB	NM_001308142.2 link	c.*464C>T		3_prime_UTR_variant	Exon 17 of 17	ENST00000571589.6	NP_001295071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRTFB	ENST00000571589.6 link	c.*464C>T		3_prime_UTR_variant	Exon 17 of 17	2	NM_001308142.2	ENSP00000459626.2

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26886

AN:

152028

Hom.:

4580

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.0319

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.0735

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.0513

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0494

Gnomad OTH

AF:

0.166

GnomAD4 exome

AF:

0.0476

AC:

AN:

1260

Hom.:

Cov.:

AF XY:

0.0437

AC XY:

AN XY:

686

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AF:

0.0608

AC:

AN:

148

Ashkenazi Jewish (ASJ)

AF:

0.0625

AC:

AN:

East Asian (EAS)

AF:

0.222

AC:

AN:

South Asian (SAS)

AF:

0.179

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0270

AC:

AN:

962

Other (OTH)

AF:

0.0667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

GnomAD4 genome

AF:

0.177

AC:

26967

AN:

152148

Hom.:

4604

Cov.:

AF XY:

0.177

AC XY:

13170

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.431

AC:

17868

AN:

41448

American (AMR)

AF:

0.130

AC:

1983

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0735

AC:

255

AN:

3468

East Asian (EAS)

AF:

0.301

AC:

1556

AN:

5178

South Asian (SAS)

AF:

0.206

AC:

994

AN:

4818

European-Finnish (FIN)

AF:

0.0513

AC:

544

AN:

10612

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0494

AC:

3362

AN:

68012

Other (OTH)

AF:

0.166

AC:

351

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

890

1780

2670

3560

4450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.0840

Hom.:

1009

Bravo

AF:

0.193

Asia WGS

AF:

0.254

AC:

885

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.077

(source)

DANN

Benign

0.64

PhyloP100

-4.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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