rs1791067

Variant names:

• chr18-3268552-T-A
• rs1791067
• NM_033546.4:c.-15-4332T>A

Your query was ambiguous. Multiple possible variants found:

• chr18-3268552-T-A
• chr18-3268552-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_033546.4(MYL12B):​c.-15-4332T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: MYL12B NM_033546.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 5 publications found

Genes affected

MYL12B (HGNC:29827): (myosin light chain 12B) The activity of nonmuscle myosin II (see MYH9; MIM 160775) is regulated by phosphorylation of a regulatory light chain, such as MRLC2. This phosphorylation results in higher MgATPase activity and the assembly of myosin II filaments (Iwasaki et al., 2001 [PubMed 11942626]).[supplied by OMIM, Mar 2008]

ENSG00000301728 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYL12B	NM_033546.4	c.-15-4332T>A		intron_variant	Intron 1 of 3	ENST00000237500.10	NP_291024.1
MYL12B	NM_001144944.1	c.-15-4332T>A		intron_variant	Intron 1 of 3		NP_001138416.1
MYL12B	NM_001144945.1	c.-15-4332T>A		intron_variant	Intron 1 of 3		NP_001138417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYL12B	ENST00000237500.10	c.-15-4332T>A		intron_variant	Intron 1 of 3	1	NM_033546.4	ENSP00000237500.5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.49
PhyloP100		0.46

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: rs1791067; hg19: chr18-3268550;