Genetic Variant MYH15:c.5632-5_5632-4insGTTTTT (chr3-108383733-T-TAAAAAC) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_014981.3(MYH15):c.5632-5_5632-4insGTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000064 in 1,094,484 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000017 ( 0 hom., cov: 29)

Exomes 𝑓: 0.0000058 ( 0 hom. )

Consequence

MYH15
NM_014981.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Variant links:

Genes affected

MYH15 (HGNC:31073): (myosin heavy chain 15) Predicted to enable several functions, including ATP binding activity; actin filament binding activity; and calmodulin binding activity. Predicted to be involved in extraocular skeletal muscle development. Located in cytosol and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

MYH15 links:

LOC124900545 (HGNC:):

LOC124900545 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MYH15	NM_014981.3 link	c.5632-5_5632-4insGTTTTT	splice_region_variant, intron_variant	Intron 39 of 40	ENST00000693548.1	NP_055796.2	Q9Y2K3
MYH15	XM_011512559.3 link	c.5692-5_5692-4insGTTTTT	splice_region_variant, intron_variant	Intron 41 of 42		XP_011510861.1	Q9Y2K3
LOC124900545	XR_007095998.1 link	n.112+2087_112+2088insCAAAAA	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MYH15	ENST00000693548.1 link	c.5632-5_5632-4insGTTTTT	splice_region_variant, intron_variant	Intron 39 of 40		NM_014981.3	ENSP00000508967.1	A0A8I5KXJ3
MYH15	ENST00000273353.5 link	c.5632-5_5632-4insGTTTTT	splice_region_variant, intron_variant	Intron 40 of 41	1		ENSP00000273353.4	Q9Y2K3
MYH15	ENST00000689784.1 link	c.4651-5_4651-4insGTTTTT	splice_region_variant, intron_variant	Intron 31 of 32			ENSP00000509841.1	A0A8I5KYE8

Frequencies

GnomAD3 genomes

AF:

0.0000168

AC:

AN:

59484

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000409

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000580

AC:

AN:

1035000

Hom.:

Cov.:

AF XY:

0.00000789

AC XY:

AN XY:

507062

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000524

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000357

Gnomad4 OTH exome

AF:

0.0000237

GnomAD4 genome

AF:

0.0000168

AC:

AN:

59484

Hom.:

Cov.:

AF XY:

0.0000356

AC XY:

AN XY:

28056

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000409

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over