3-108383733-T-TAAAAAC

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]

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 HGVSp Effect Exon rank MANE Protein UniProt
MYH15NM_014981.3 linkc.5632-5_5632-4insGTTTTT splice_region_variant, intron_variant Intron 39 of 40 ENST00000693548.1 NP_055796.2 Q9Y2K3
MYH15XM_011512559.3 linkc.5692-5_5692-4insGTTTTT splice_region_variant, intron_variant Intron 41 of 42 XP_011510861.1 Q9Y2K3
LOC124900545XR_007095998.1 linkn.112+2087_112+2088insCAAAAA intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYH15ENST00000693548.1 linkc.5632-5_5632-4insGTTTTT splice_region_variant, intron_variant Intron 39 of 40 NM_014981.3 ENSP00000508967.1 A0A8I5KXJ3
MYH15ENST00000273353.5 linkc.5632-5_5632-4insGTTTTT splice_region_variant, intron_variant Intron 40 of 41 1 ENSP00000273353.4 Q9Y2K3
MYH15ENST00000689784.1 linkc.4651-5_4651-4insGTTTTT splice_region_variant, intron_variant Intron 31 of 32 ENSP00000509841.1 A0A8I5KYE8

Frequencies

GnomAD3 genomes
AF:
0.0000168
AC:
1
AN:
59484
Hom.:
0
Cov.:
29
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:
6
AN:
1035000
Hom.:
0
Cov.:
31
AF XY:
0.00000789
AC XY:
4
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:
1
AN:
59484
Hom.:
0
Cov.:
29
AF XY:
0.0000356
AC XY:
1
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.

Other links and lift over

dbSNP: rs377049870; hg19: chr3-108102580; API