rs4267326

chr16-14185180-G-A

Variant summary

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

The NM_001308142.2(MRTFB):c.155-25063G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 152,220 control chromosomes in the GnomAD database, including 1,218 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 0.088 (1218 hom., cov: 32)
• Consequence: MRTFB NM_001308142.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRTFB	NM_001308142.2	c.155-25063G>A		intron_variant		ENST00000571589.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRTFB	ENST00000571589.6	c.155-25063G>A		intron_variant		2	NM_001308142.2	P4

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 13406 AN: 152102 Hom.: 1208 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.00923

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0891

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

GnomAD4 genome AF: 0.0884 AC: 13461 AN: 152220 Hom.: 1218 Cov.: 32 AF XY: 0.0870 AC XY: 6476 AN XY: 74446

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0234

Gnomad4 FIN AF: 0.00923

Gnomad4 NFE AF: 0.0347

Gnomad4 OTH AF: 0.0882

Alfa AF: 0.0706 Hom.: 137

Bravo AF: 0.0994

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.57
Dann	Benign	0.68

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: rs4267326; hg19: chr16-14279037;