rs2288433

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012334.3(MYO10):​c.4385-559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,076 control chromosomes in the GnomAD database, including 7,569 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 0.31 ( 7569 hom., cov: 32)

Consequence

MYO10
NM_012334.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.548
Variant links:
Genes affected
MYO10 (HGNC:7593): (myosin X) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-10 (MYH10). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. This gene functions as an actin-based molecular motor and plays a role in integration of F-actin and microtubule cytoskeletons during meiosis. [provided by RefSeq, Dec 2011]
RETREG1-AS1 (HGNC:55551): (RETREG1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYO10NM_012334.3 linkuse as main transcriptc.4385-559G>A intron_variant ENST00000513610.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYO10ENST00000513610.6 linkuse as main transcriptc.4385-559G>A intron_variant 1 NM_012334.3 P1Q9HD67-1
RETREG1-AS1ENST00000653650.1 linkuse as main transcriptn.652C>T non_coding_transcript_exon_variant 3/3

Frequencies

GnomAD3 genomes
AF:
0.313
AC:
47525
AN:
151958
Hom.:
7557
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.318
Gnomad AMI
AF:
0.391
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.314
Gnomad EAS
AF:
0.255
Gnomad SAS
AF:
0.412
Gnomad FIN
AF:
0.302
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.314
Gnomad OTH
AF:
0.305
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.313
AC:
47575
AN:
152076
Hom.:
7569
Cov.:
32
AF XY:
0.313
AC XY:
23240
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.318
Gnomad4 AMR
AF:
0.287
Gnomad4 ASJ
AF:
0.314
Gnomad4 EAS
AF:
0.255
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.302
Gnomad4 NFE
AF:
0.314
Gnomad4 OTH
AF:
0.309
Alfa
AF:
0.316
Hom.:
15584
Bravo
AF:
0.314
Asia WGS
AF:
0.319
AC:
1109
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.57
DANN
Benign
0.22

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

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

Other links and lift over

dbSNP: rs2288433; hg19: chr5-16680772; API