16-14261908-C-T

Position:

• chr16-14261908-C-T

Variant summary

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

The NM_001308142.2(MRTFB):​c.*464C>T variant causes a 3 prime UTR 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 NM_001308142.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.07

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=-0.93).
• 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/exons	MANE	Protein	UniProt
MRTFB	NM_001308142.2	c.*464C>T		3_prime_UTR_variant	17/17	ENST00000571589.6	NP_001295071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRTFB	ENST00000571589.6	c.*464C>T		3_prime_UTR_variant	17/17	2	NM_001308142.2	ENSP00000459626	P4
MRTFB	ENST00000572588.1	n.3032C>T		non_coding_transcript_exon_variant	5/5	1
MRTFB	ENST00000318282.9	c.*464C>T		3_prime_UTR_variant	16/16	5		ENSP00000339086	A2
MRTFB	ENST00000571770.1	c.*58+406C>T		intron_variant, NMD_transcript_variant		5		ENSP00000459518

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26886 AN: 152028 Hom.: 4580 Cov.: 33

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: 60 AN: 1260 Hom.: 8 Cov.: 0 AF XY: 0.0437 AC XY: 30 AN XY: 686

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 0.0608

Gnomad4 ASJ exome AF: 0.0625

Gnomad4 EAS exome AF: 0.222

Gnomad4 SAS exome AF: 0.179

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0270

Gnomad4 OTH exome AF: 0.0667

GnomAD4 genome AF: 0.177 AC: 26967 AN: 152148 Hom.: 4604 Cov.: 33 AF XY: 0.177 AC XY: 13170 AN XY: 74382

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0735

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.0513

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0818 Hom.: 734

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
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs30126; hg19: chr16-14355765;