rs220076

chr20-36544154-C-Achr20-36544154-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MYL9	NM_006097.5	c.-26-705C>A		intron_variant		ENST00000279022.7
DLGAP4-AS1	NR_109939.1	n.467+27287G>T		intron_variant, non_coding_transcript_variant
MYL9	NM_181526.3	c.-26-705C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL9	ENST00000279022.7	c.-26-705C>A		intron_variant		1	NM_006097.5	P1
MYL9	ENST00000346786.2	c.-26-705C>A		intron_variant		1
DLGAP4-AS1	ENST00000425233.6	n.580-16230G>T		intron_variant, non_coding_transcript_variant		5
DLGAP4-AS1	ENST00000439595.5	n.467+27287G>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.671

Alfa AF: 0.725 Hom.: 18662

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs220076; hg19: chr20-35172557;