rs756472

chr16-14185624-G-Achr16-14185624-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001308142.2(MRTFB):c.155-24619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,246 control chromosomes in the GnomAD database, including 7,814 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 0.23 (7814 hom., cov: 31)
• Consequence: MRTFB NM_001308142.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRTFB	NM_001308142.2	c.155-24619G>A		intron_variant		ENST00000571589.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRTFB	ENST00000571589.6	c.155-24619G>A		intron_variant		2	NM_001308142.2	P4

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35185 AN: 151130 Hom.: 7779 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 35280 AN: 151246 Hom.: 7814 Cov.: 31 AF XY: 0.233 AC XY: 17229 AN XY: 73838

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0530

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.228

Alfa AF: 0.0533 Hom.: 128

Bravo AF: 0.255

Asia WGS AF: 0.260 AC: 904 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.14
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs756472; hg19: chr16-14279481;