rs756472

Variant names:

• chr16-14185624-G-A
• rs756472
• NM_001308142.2:c.155-24619G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-14185624-G-A
• chr16-14185624-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MRTFB	NM_001308142.2	c.155-24619G>A		intron_variant	Intron 3 of 16	ENST00000571589.6	NP_001295071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRTFB	ENST00000571589.6	c.155-24619G>A		intron_variant	Intron 3 of 16	2	NM_001308142.2	ENSP00000459626.2

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

African (AFR) AF: 0.574 AC: 23657 AN: 41210

American (AMR) AF: 0.170 AC: 2583 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3464

East Asian (EAS) AF: 0.292 AC: 1495 AN: 5122

South Asian (SAS) AF: 0.224 AC: 1071 AN: 4784

European-Finnish (FIN) AF: 0.0530 AC: 548 AN: 10332

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4847 AN: 67838

Other (OTH) AF: 0.228 AC: 478 AN: 2096

Alfa AF: 0.0771 Hom.: 249

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
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs756472; hg19: chr16-14279481;