20-36544154-C-A

Variant names:

• chr20-36544154-C-A
• rs220076
• NM_006097.5:c.-26-705C>A

Variant summary

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

The NM_006097.5(MYL9):​c.-26-705C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,012 control chromosomes in the GnomAD database, including 32,390 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 0.63 (32390 hom., cov: 32)
• Consequence: MYL9 NM_006097.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 6 publications found

Genes affected

MYL9 (HGNC:15754): (myosin light chain 9) Myosin, a structural component of muscle, consists of two heavy chains and four light chains. The protein encoded by this gene is a myosin light chain that may regulate muscle contraction by modulating the ATPase activity of myosin heads. The encoded protein binds calcium and is activated by myosin light chain kinase. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

DLGAP4-AS1 (HGNC:51223): (DLGAP4 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYL9	NM_006097.5	c.-26-705C>A		intron_variant	Intron 1 of 3	ENST00000279022.7	NP_006088.2
MYL9	NM_181526.3	c.-26-705C>A		intron_variant	Intron 1 of 2		NP_852667.1
DLGAP4-AS1	NR_109939.1	n.467+27287G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYL9	ENST00000279022.7	c.-26-705C>A		intron_variant	Intron 1 of 3	1	NM_006097.5	ENSP00000279022.2

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95534 AN: 151894 Hom.: 32404 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.628 AC: 95532 AN: 152012 Hom.: 32390 Cov.: 32 AF XY: 0.624 AC XY: 46388 AN XY: 74310

African (AFR) AF: 0.372 AC: 15401 AN: 41440

American (AMR) AF: 0.583 AC: 8902 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2698 AN: 3470

East Asian (EAS) AF: 0.599 AC: 3098 AN: 5168

South Asian (SAS) AF: 0.625 AC: 3008 AN: 4814

European-Finnish (FIN) AF: 0.711 AC: 7526 AN: 10582

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52533 AN: 67958

Other (OTH) AF: 0.671 AC: 1415 AN: 2108

Alfa AF: 0.724 Hom.: 20930

Bravo AF: 0.608

Asia WGS AF: 0.559 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.55
PhyloP100		1.8
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: rs220076; hg19: chr20-35172557;