rs17283597

Variant names:

• chr3-152260770-A-G
• rs17283597
• NM_001376819.1:c.-790+16330A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001376819.1(MBNL1):​c.-790+16330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 152,218 control chromosomes in the GnomAD database, including 690 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 0.086 (690 hom., cov: 32)
• Consequence: MBNL1 NM_001376819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 2 publications found

Genes affected

MBNL1 (HGNC:6923): (muscleblind like splicing regulator 1) This gene encodes a member of the muscleblind protein family which was initially described in Drosophila melanogaster. The encoded protein is a C3H-type zinc finger protein that modulates alternative splicing of pre-mRNAs. Muscleblind proteins bind specifically to expanded dsCUG RNA but not to normal size CUG repeats and may thereby play a role in the pathophysiology of myotonic dystrophy. Mice lacking this gene exhibited muscle abnormalities and cataracts. Several alternatively spliced transcript variants have been described but the full-length natures of only some have been determined. The different isoforms are thought to have different binding specificities and/or splicing activities. [provided by RefSeq, Sep 2015]

MBNL1-AS1 (HGNC:44584): (MBNL1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBNL1	NM_001376819.1	c.-790+16330A>G		intron_variant	Intron 2 of 12		NP_001363748.1
MBNL1	NM_001387781.1	c.-790+16330A>G		intron_variant	Intron 2 of 11		NP_001374710.1
MBNL1	NM_001387785.1	c.-790+16330A>G		intron_variant	Intron 2 of 11		NP_001374714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MBNL1	ENST00000477171.1	n.333+16330A>G		intron_variant	Intron 2 of 2	3
MBNL1-AS1	ENST00000669594.1	n.291+6638T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0856 AC: 13014 AN: 152100 Hom.: 688 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0111

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0856 AC: 13026 AN: 152218 Hom.: 690 Cov.: 32 AF XY: 0.0851 AC XY: 6335 AN XY: 74440

African (AFR) AF: 0.0347 AC: 1441 AN: 41544

American (AMR) AF: 0.0776 AC: 1186 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5190

South Asian (SAS) AF: 0.0704 AC: 340 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1137 AN: 10596

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8139 AN: 67984

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.110 Hom.: 953

Bravo AF: 0.0807

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.20
DANN	Benign	0.68
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs17283597; hg19: chr3-151978559;