5-16933528-T-C

Variant names:

• chr5-16933528-T-C
• rs31463
• NM_012334.3:c.21+2260A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012334.3(MYO10):​c.21+2260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,068 control chromosomes in the GnomAD database, including 12,153 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 0.40 (12153 hom., cov: 33)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.21+2260A>G		intron_variant	Intron 1 of 40	ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.21+2260A>G		intron_variant	Intron 1 of 39		XP_006714538.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.21+2260A>G		intron_variant	Intron 1 of 40	1	NM_012334.3	ENSP00000421280.1
MYO10	ENST00000507288.1	c.21+2260A>G		intron_variant	Intron 1 of 3	1		ENSP00000426664.1
MYO10	ENST00000274203.13	c.21+2260A>G		intron_variant	Intron 1 of 40	5		ENSP00000274203.10
MYO10	ENST00000502436.5	c.21+2260A>G		intron_variant	Intron 1 of 5	5		ENSP00000426783.2

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60124 AN: 151948 Hom.: 12159 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.395 AC: 60119 AN: 152068 Hom.: 12153 Cov.: 33 AF XY: 0.389 AC XY: 28944 AN XY: 74332

African (AFR) AF: 0.424 AC: 17604 AN: 41486

American (AMR) AF: 0.317 AC: 4837 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1689 AN: 3464

East Asian (EAS) AF: 0.310 AC: 1605 AN: 5176

South Asian (SAS) AF: 0.428 AC: 2066 AN: 4824

European-Finnish (FIN) AF: 0.322 AC: 3393 AN: 10550

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27465 AN: 67972

Other (OTH) AF: 0.384 AC: 811 AN: 2112

Alfa AF: 0.406 Hom.: 6979

Bravo AF: 0.395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.088
DANN	Benign	0.47
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs31463; hg19: chr5-16933637;