rs3934861

Variant names:

• chr1-24105466-G-A
• rs3934861
• NM_152372.4:c.560+454C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-24105466-G-A
• chr1-24105466-G-C

Variant summary

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

The NM_152372.4(MYOM3):​c.560+454C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,148 control chromosomes in the GnomAD database, including 22,554 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 0.54 (22554 hom., cov: 33)
• Consequence: MYOM3 NM_152372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 12 publications found

Genes affected

MYOM3 (HGNC:26679): (myomesin 3) Predicted to enable actin filament binding activity and protein homodimerization activity. Predicted to be involved in muscle contraction. Predicted to be active in M band. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152372.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOM3	NM_152372.4	MANE Select	c.560+454C>T		intron	N/A	NP_689585.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOM3	ENST00000374434.4	TSL:1 MANE Select	c.560+454C>T		intron	N/A	ENSP00000363557.3	Q5VTT5-1
	MYOM3	ENST00000958997.1		c.560+454C>T		intron	N/A	ENSP00000629056.1
	MYOM3	ENST00000959000.1		c.560+454C>T		intron	N/A	ENSP00000629059.1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81355 AN: 152030 Hom.: 22512 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.535 AC: 81461 AN: 152148 Hom.: 22554 Cov.: 33 AF XY: 0.532 AC XY: 39590 AN XY: 74394

African (AFR) AF: 0.665 AC: 27618 AN: 41528

American (AMR) AF: 0.435 AC: 6654 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1639 AN: 5162

South Asian (SAS) AF: 0.408 AC: 1971 AN: 4826

European-Finnish (FIN) AF: 0.583 AC: 6172 AN: 10584

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 34024 AN: 67972

Other (OTH) AF: 0.527 AC: 1113 AN: 2112

Alfa AF: 0.502 Hom.: 61949

Bravo AF: 0.530

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.058
DANN	Benign	0.62
PhyloP100		-0.46
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: rs3934861; hg19: chr1-24431956;