rs2288433

Positions:

• chr5-16680663-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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)

ACMG classification

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
MYO10	NM_012334.3	c.4385-559G>A		intron_variant		ENST00000513610.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO10	ENST00000513610.6	c.4385-559G>A		intron_variant		1	NM_012334.3	P1
RETREG1-AS1	ENST00000653650.1	n.652C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47525 AN: 151958 Hom.: 7557 Cov.: 32

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

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

Other links and lift over

dbSNP: rs2288433; hg19: chr5-16680772;