rs25910

chr5-16694200-T-Cchr5-16694200-T-G

Variant summary

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

The NM_012334.3(MYO10):c.3800+171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,122 control chromosomes in the GnomAD database, including 27,175 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 0.59 (27175 hom., cov: 33)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO10	NM_012334.3	c.3800+171A>G		intron_variant		ENST00000513610.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO10	ENST00000513610.6	c.3800+171A>G		intron_variant		1	NM_012334.3	P1
MYO10	ENST00000274203.13	c.3833+171A>G		intron_variant		5
MYO10	ENST00000505695.5	c.1817+171A>G		intron_variant		2
MYO10	ENST00000515803.5	c.1817+171A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89894 AN: 152004 Hom.: 27128 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.592 AC: 90004 AN: 152122 Hom.: 27175 Cov.: 33 AF XY: 0.594 AC XY: 44157 AN XY: 74346

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.592

Alfa AF: 0.536 Hom.: 43440

Bravo AF: 0.595

Asia WGS AF: 0.554 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs25910; hg19: chr5-16694309; COSMIC: COSV57022489;